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J. Andrew Mccammon

Title(s)Professor, Pharmacology
SchoolAcademic Aff
Phone858-534-2905
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    Collapse Biography 
    Collapse Education and Training
    Harvard UniversityPh.D.1976Chemical Physics
    Pomona CollegeB.A.1969Chemistry, Mathematics and Physics
    Collapse Awards and Honors
    University of Kansas2020Newmark Award and Lecture
    BU, Harvard, MIT2019Student-organized Theoretical Chemistry Lecture Series
    Ohio State University2017Russell M. Pitzer Award and Lecture in Theoretical Chemistry
    University of Wisconsin2016  - 2017Hirschfelder Prize in Theoretical Chemistry
    US National Academy of Sciences2011Member
    American Chemical Society2008National Award for Computers in Chemical and Pharmaceutical Research
    American Academy of Arts and Sciences2006Fellow
    Howard Hughes Medical Institute2000Investigator
    Smithsonian Institution1995Award for Breakthrough Computational Science
    Burroughs Wellcome Fund1987  - 1992G.H. Hitchings Award for Innovative Methods in Drug Design
    1982  - 1987Camille and Henry Dreyfus Teacher–Scholar Award
    1980  - 1985NIH Research Career Development Award
    1980  - 1984Alfred P. Sloan Research Fellow

    Collapse Overview 

    Collapse Research 
    Collapse Research Activities and Funding
    Protein-Protein Interaction in Natural Product Biosynthesis
    NIH/NIGMS R01GM095970Mar 1, 2012 - Jan 31, 2020
    Role: Principal Investigator
    Theory of Biomolecular Diffusion
    NIH/NIGMS R01GM031749Jun 1, 1983 - Jun 30, 2023
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Websites

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Sztain T, Bartholow TG, McCammon JA, Burkart MD. Shifting the Hydrolysis Equilibrium of Substrate Loaded Acyl Carrier Proteins. Biochemistry. 2019 Aug 14. PMID: 31397556.
      View in: PubMed
    2. Zhou S, Weiß RG, Cheng LT, Dzubiella J, McCammon JA, Li B. Variational implicit-solvent predictions of the dry-wet transition pathways for ligand-receptor binding and unbinding kinetics. Proc Natl Acad Sci U S A. 2019 Jul 03. PMID: 31270236.
      View in: PubMed
    3. Sztain T, Patel A, Lee DJ, Davis T, McCammon JA, Burkart MD. One atom matters: modifying the thioester linkage affects structure of the acyl carrier protein. Angew Chem Int Ed Engl. 2019 May 28. PMID: 31140212.
      View in: PubMed
    4. Dodge GJ, Patel A, Jaremko KL, McCammon JA, Smith JL, Burkart MD. Structural and dynamical rationale for fatty acid unsaturation in Escherichia coli. Proc Natl Acad Sci U S A. 2019 04 02; 116(14):6775-6783. PMID: 30872475.
      View in: PubMed
    5. Ricci CG, Chen JS, Miao Y, Jinek M, Doudna JA, McCammon JA, Palermo G. Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics. ACS Cent Sci. 2019 Apr 24; 5(4):651-662. PMID: 31041385.
      View in: PubMed
    6. Huang YM, Munguia J, Miao Y, Nizet V, McCammon JA. Docking simulation and antibiotic discovery targeting the MlaC protein in Gram-negative bacteria. Chem Biol Drug Des. 2019 Apr; 93(4):647-652. PMID: 30570806.
      View in: PubMed
    7. Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, Cecchini M, Changeux JP, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Di Pizio A, Niv MY, Nussinov R, Tsai CJ, Jang H, Padhorny D, Kozakov D, McLeish T. Allostery in Its Many Disguises: From Theory to Applications. Structure. 2019 Apr 02; 27(4):566-578. PMID: 30744993.
      View in: PubMed
    8. Feher VA, Schiffer JM, Mermelstein DJ, Mih N, Pierce LCT, McCammon JA, Amaro RE. Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant. Biophys J. 2019 Jan 22; 116(2):205-214. PMID: 30606449.
      View in: PubMed
    9. Kim WE, Patel A, Hur GH, Tufar P, Wuo MG, McCammon JA, Burkart MD. Mechanistic Probes for the Epimerization Domain of Nonribosomal Peptide Synthetases. Chembiochem. 2019 Jan 18; 20(2):147-152. PMID: 30194895.
      View in: PubMed
    10. Zhang J, Wang N, Miao Y, Hauser F, McCammon JA, Rappel WJ, Schroeder JI. Identification of SLAC1 anion channel residues required for CO2/bicarbonate sensing and regulation of stomatal movements. Proc Natl Acad Sci U S A. 2018 10 30; 115(44):11129-11137. PMID: 30301791.
      View in: PubMed
    11. Ricci CG, McCammon JA. Heterogeneous Solvation in Distinctive Protein-Protein Interfaces Revealed by Molecular Dynamics Simulations. J Phys Chem B. 2018 Dec 13; 122(49):11695-11701. PMID: 30252476.
      View in: PubMed
    12. Utesch T, de Miguel Catalina A, Schattenberg C, Paege N, Schmieder P, Krause E, Miao Y, McCammon JA, Meyer V, Jung S, Mroginski MA. A Computational Modeling Approach Predicts Interaction of the Antifungal Protein AFP from Aspergillus giganteus with Fungal Membranes via Its ?-Core Motif. mSphere. 2018 10 03; 3(5). PMID: 30282755.
      View in: PubMed
    13. Mermelstein DJ, McCammon JA, Walker RC. pH-dependent conformational dynamics of beta-secretase 1: A molecular dynamics study. J Mol Recognit. 2019 Mar; 32(3):e2765. PMID: 30264484.
      View in: PubMed
    14. Palermo G, Chen JS, Ricci CG, Rivalta I, Jinek M, Batista VS, Doudna JA, McCammon JA. Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain. Q Rev Biophys. 2018; 51. PMID: 30555184.
      View in: PubMed
    15. Amaro RE, Baudry J, Chodera J, Demir Ö, McCammon JA, Miao Y, Smith JC. Ensemble Docking in Drug Discovery. Biophys J. 2018 May 22; 114(10):2271-2278. PMID: 29606412.
      View in: PubMed
    16. Mermelstein DJ, Lin C, Nelson G, Kretsch R, McCammon JA, Walker RC. Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package. J Comput Chem. 2018 Jul 15; 39(19):1354-1358. PMID: 29532496.
      View in: PubMed
    17. Huang YM, McCammon JA, Miao Y. Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation. J Chem Theory Comput. 2018 Apr 10; 14(4):1853-1864. PMID: 29489349.
      View in: PubMed
    18. Miao Y, McCammon JA. Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor. Proc Natl Acad Sci U S A. 2018 03 20; 115(12):3036-3041. PMID: 29507218.
      View in: PubMed
    19. Mouchlis VD, Chen Y, McCammon JA, Dennis EA. Membrane Allostery and Unique Hydrophobic Sites Promote Enzyme Substrate Specificity. J Am Chem Soc. 2018 03 07; 140(9):3285-3291. PMID: 29342349.
      View in: PubMed
    20. Guan W, Cheng X, Huang J, Huber G, Li W, McCammon JA, Zhang B. RPYFMM: Parallel Adaptive Fast Multipole Method for Rotne-Prager-Yamakawa Tensor in Biomolecular Hydrodynamics Simulations. Comput Phys Commun. 2018 Jun; 227:99-108. PMID: 30147116.
      View in: PubMed
    21. Miao Y, Huang YM, Walker RC, McCammon JA, Chang CA. Ligand Binding Pathways and Conformational Transitions of the HIV Protease. Biochemistry. 2018 03 06; 57(9):1533-1541. PMID: 29394043.
      View in: PubMed
    22. Ricci CG, Li B, Cheng LT, Dzubiella J, McCammon JA. Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly. Front Mol Biosci. 2018; 5:13. PMID: 29484300.
      View in: PubMed
    23. Venkatramani A, Gravina Ricci C, Oldfield E, McCammon JA. Remarkable similarity in Plasmodium falciparum and Plasmodium vivax geranylgeranyl diphosphate synthase dynamics and its implication for antimalarial drug design. Chem Biol Drug Des. 2018 Jun; 91(6):1068-1077. PMID: 29345110.
      View in: PubMed
    24. Huang YM, Huber GA, Wang N, Minteer SD, McCammon JA. Brownian dynamic study of an enzyme metabolon in the TCA cycle: Substrate kinetics and channeling. Protein Sci. 2018 02; 27(2):463-471. PMID: 29094409.
      View in: PubMed
    25. Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei GW, Holst MJ, McCammon JA, Baker NA. Improvements to the APBS biomolecular solvation software suite. Protein Sci. 2018 01; 27(1):112-128. PMID: 28836357.
      View in: PubMed
    26. Jaremko MJ, Lee DJ, Patel A, Winslow V, Opella SJ, McCammon JA, Burkart MD. Manipulating Protein-Protein Interactions in Nonribosomal Peptide Synthetase Type II Peptidyl Carrier Proteins. Biochemistry. 2017 10 10; 56(40):5269-5273. PMID: 28920687.
      View in: PubMed
    27. Miao Y, McCammon JA. Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications. Annu Rep Comput Chem. 2017; 13:231-278. PMID: 29720925.
      View in: PubMed
    28. Palermo G, Ricci CG, Fernando A, Basak R, Jinek M, Rivalta I, Batista VS, McCammon JA. Protospacer Adjacent Motif-Induced Allostery Activates CRISPR-Cas9. J Am Chem Soc. 2017 11 15; 139(45):16028-16031. PMID: 28764328.
      View in: PubMed
    29. Caliman AD, Miao Y, McCammon JA. Mapping the allosteric sites of the A2A adenosine receptor. Chem Biol Drug Des. 2018 01; 91(1):5-16. PMID: 28639411.
      View in: PubMed
    30. Ricci CG, Li B, Cheng LT, Dzubiella J, McCammon JA. "Martinizing" the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins. J Phys Chem B. 2017 07 13; 121(27):6538-6548. PMID: 28613904.
      View in: PubMed
    31. Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Proc Natl Acad Sci U S A. 2017 07 11; 114(28):7260-7265. PMID: 28652374.
      View in: PubMed
    32. Caliman AD, Miao Y, McCammon JA. Activation mechanisms of the first sphingosine-1-phosphate receptor. Protein Sci. 2017 06; 26(6):1150-1160. PMID: 28370663.
      View in: PubMed
    33. Dick BL, Patel A, McCammon JA, Cohen SM. Effect of donor atom identity on metal-binding pharmacophore coordination. J Biol Inorg Chem. 2017 Jun; 22(4):605-613. PMID: 28389830.
      View in: PubMed
    34. O'Dowd B, Williams S, Wang H, No JH, Rao G, Wang W, McCammon JA, Cramer SP, Oldfield E. Spectroscopic and Computational Investigations of Ligand Binding to IspH: Discovery of Non-diphosphate Inhibitors. Chembiochem. 2017 05 18; 18(10):914-920. PMID: 28253432.
      View in: PubMed
    35. Chan AH, Yi SW, Weiner EM, Amer BR, Sue CK, Wereszczynski J, Dillen CA, Senese S, Torres JZ, McCammon JA, Miller LS, Jung ME, Clubb RT. NMR structure-based optimization of Staphylococcus aureus sortase A pyridazinone inhibitors. Chem Biol Drug Des. 2017 Sep; 90(3):327-344. PMID: 28160417.
      View in: PubMed
    36. Pang YT, Miao Y, Wang Y, McCammon JA. Gaussian Accelerated Molecular Dynamics in NAMD. J Chem Theory Comput. 2017 01 10; 13(1):9-19. PMID: 28034310.
      View in: PubMed
    37. Miao Y, McCammon JA. Graded activation and free energy landscapes of a muscarinic G-protein-coupled receptor. Proc Natl Acad Sci U S A. 2016 10 25; 113(43):12162-12167. PMID: 27791003.
      View in: PubMed
    38. Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations. ACS Cent Sci. 2016 Oct 26; 2(10):756-763. PMID: 27800559.
      View in: PubMed
    39. Miao Y, Goldfeld DA, Moo EV, Sexton PM, Christopoulos A, McCammon JA, Valant C. Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor. Proc Natl Acad Sci U S A. 2016 09 20; 113(38):E5675-84. PMID: 27601651.
      View in: PubMed
    40. G Ricci C, Liu YL, Zhang Y, Wang Y, Zhu W, Oldfield E, McCammon JA. Dynamic Structure and Inhibition of a Malaria Drug Target: Geranylgeranyl Diphosphate Synthase. Biochemistry. 2016 09 13; 55(36):5180-90. PMID: 27564465.
      View in: PubMed
    41. McCammon JA. Autobiography of J. Andrew McCammon. J Phys Chem B. 2016 08 25; 120(33):8057-60. PMID: 27558539.
      View in: PubMed
    42. Zhou S, Sun H, Cheng LT, Dzubiella J, Li B, McCammon JA. Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations. J Chem Phys. 2016 Aug 07; 145(5):054114. PMID: 27497546; PMCID: PMC4975753 [Available on 08/07/17].
    43. Miao Y, McCammon JA. Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review. Mol Simul. 2016; 42(13):1046-1055. PMID: 27453631.
      View in: PubMed
    44. Miao Y, McCammon JA. G-protein coupled receptors: advances in simulation and drug discovery. Curr Opin Struct Biol. 2016 12; 41:83-89. PMID: 27344006.
      View in: PubMed
    45. Huang YM, Miao Y, Munguia J, Lin L, Nizet V, McCammon JA. Molecular dynamic study of MlaC protein in Gram-negative bacteria: conformational flexibility, solvent effect and protein-phospholipid binding. Protein Sci. 2016 08; 25(8):1430-7. PMID: 27111825; PMCID: PMC4972199 [Available on 08/01/17].
    46. Mouchlis VD, Morisseau C, Hammock BD, Li S, McCammon JA, Dennis EA. Computer-aided drug design guided by hydrogen/deuterium exchange mass spectrometry: A powerful combination for the development of potent and selective inhibitors of Group VIA calcium-independent phospholipase A2. Bioorg Med Chem. 2016 10 15; 24(20):4801-4811. PMID: 27320659.
      View in: PubMed
    47. Huber GA, Miao Y, Zhou S, Li B, McCammon JA. Hybrid finite element and Brownian dynamics method for charged particles. J Chem Phys. 2016 Apr 28; 144(16):164107. PMID: 27131531; PMCID: PMC4851620 [Available on 04/28/17].
    48. Mouchlis VD, Limnios D, Kokotou MG, Barbayianni E, Kokotos G, McCammon JA, Dennis EA. Development of Potent and Selective Inhibitors for Group VIA Calcium-Independent Phospholipase A2 Guided by Molecular Dynamics and Structure-Activity Relationships. J Med Chem. 2016 05 12; 59(9):4403-14. PMID: 27087127; PMCID: PMC4946799 [Available on 05/12/17].
    49. Miao Y, Baudry J, Smith JC, McCammon JA. General trends of dihedral conformational transitions in a globular protein. Proteins. 2016 Apr; 84(4):501-14. PMID: 26799251.
      View in: PubMed
    50. Kim MO, McCammon JA. Computation of pH-dependent binding free energies. Biopolymers. 2016 Jan; 105(1):43-9. PMID: 26202905; PMCID: PMC4623928 [Available on 01/01/17].
    51. Sun H, Wen J, Zhao Y, Li B, McCammon JA. A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics. J Chem Phys. 2015 Dec 28; 143(24):243110. PMID: 26723595.
      View in: PubMed
    52. Feng X, Zhu W, Schurig-Briccio LA, Lindert S, Shoen C, Hitchings R, Li J, Wang Y, Baig N, Zhou T, Kim BK, Crick DC, Cynamon M, McCammon JA, Gennis RB, Oldfield E. Antiinfectives targeting enzymes and the proton motive force. Proc Natl Acad Sci U S A. 2015 Dec 22; 112(51):E7073-82. PMID: 26644565; PMCID: PMC4697371.
    53. Kappel K, Miao Y, McCammon JA. Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor. Q Rev Biophys. 2015 Nov; 48(4):479-87. PMID: 26537408.
      View in: PubMed
    54. Kim MO, Blachly PG, McCammon JA. Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria. PLoS Comput Biol. 2015 Oct; 11(10):e1004341. PMID: 26506513.
      View in: PubMed
    55. Cheng Y, Rao V, Tu AY, Lindert S, Wang D, Oxenford L, McCulloch AD, McCammon JA, Regnier M. Troponin I Mutations R146G and R21C Alter Cardiac Troponin Function, Contractile Properties, and Modulation by Protein Kinase A (PKA)-mediated Phosphorylation. J Biol Chem. 2015 Nov 13; 290(46):27749-66. PMID: 26391394; PMCID: PMC4646022 [Available on 11/13/16].
    56. Huang YM, Huber G, McCammon JA. Electrostatic steering enhances the rate of cAMP binding to phosphodiesterase: Brownian dynamics modeling. Protein Sci. 2015 Nov; 24(11):1884-9. PMID: 26346301; PMCID: PMC4622220 [Available on 11/01/16].
    57. Kekenes-Huskey PM, Eun C, McCammon JA. Enzyme localization, crowding, and buffers collectively modulate diffusion-influenced signal transduction: Insights from continuum diffusion modeling. J Chem Phys. 2015 Sep 07; 143(9):094103. PMID: 26342355; PMCID: PMC4560719.
    58. Miao Y, Feher VA, McCammon JA. Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation. J Chem Theory Comput. 2015 Aug 11; 11(8):3584-3595. PMID: 26300708.
      View in: PubMed
    59. Wang N, McCammon JA. Substrate channeling between the human dihydrofolate reductase and thymidylate synthase. Protein Sci. 2016 Jan; 25(1):79-86. PMID: 26096018; PMCID: PMC4815301 [Available on 01/01/17].
    60. Blachly PG, Sandala GM, Giammona DA, Bashford D, McCammon JA, Noodleman L. Broken-Symmetry DFT Computations for the Reaction Pathway of IspH, an Iron-Sulfur Enzyme in Pathogenic Bacteria. Inorg Chem. 2015 Jul 06; 54(13):6439-61. PMID: 26098647; PMCID: PMC4568833.
    61. Miao Y, Feixas F, Eun C, McCammon JA. Accelerated molecular dynamics simulations of protein folding. J Comput Chem. 2015 Jul 30; 36(20):1536-49. PMID: 26096263; PMCID: PMC4487363.
    62. Kaus JW, Harder E, Lin T, Abel R, McCammon JA, Wang L. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations. J Chem Theory Comput. 2015 Jun 09; 11(6):2670-9. PMID: 26085821.
      View in: PubMed
    63. Kaus JW, McCammon JA. Enhanced ligand sampling for relative protein-ligand binding free energy calculations. J Phys Chem B. 2015 May 21; 119(20):6190-7. PMID: 25906170; PMCID: PMC4442669.
    64. Caliman AD, Swift SE, Wang Y, Miao Y, McCammon JA. Investigation of the conformational dynamics of the apo A2A adenosine receptor. Protein Sci. 2015 Jun; 24(6):1004-12. PMID: 25761901; PMCID: PMC4456113.
    65. Miao Y, Caliman AD, McCammon JA. Allosteric effects of sodium ion binding on activation of the m3 muscarinic g-protein-coupled receptor. Biophys J. 2015 Apr 07; 108(7):1796-1806. PMID: 25863070.
      View in: PubMed
    66. Kekenes-Huskey PM, Gillette AK, McCammon JA. Erratum: "Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation" [J. Chem. Phys. 140, 174106 (2014)]. J Chem Phys. 2015 Mar 14; 142(10):109902. PMID: 25770569.
      View in: PubMed
    67. Zhou S, Cheng LT, Sun H, Che J, Dzubiella J, Li B, McCammon JA. LS-VISM: A software package for analysis of biomolecular solvation. J Comput Chem. 2015 May 30; 36(14):1047-59. PMID: 25766844; PMCID: PMC4412808.
    68. Lindert S, McCammon JA. Improved cryoEM-Guided Iterative Molecular Dynamics--Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction. J Chem Theory Comput. 2015 Mar 10; 11(3):1337-46. PMID: 25883538; PMCID: PMC4393324.
    69. Guo Z, Li B, Cheng LT, Zhou S, McCammon JA, Che J. Identification of protein-ligand binding sites by the level-set variational implicit-solvent approach. J Chem Theory Comput. 2015 Feb 10; 11(2):753-65. PMID: 25941465.
      View in: PubMed
    70. Mouchlis VD, Bucher D, McCammon JA, Dennis EA. Membranes serve as allosteric activators of phospholipase A2, enabling it to extract, bind, and hydrolyze phospholipid substrates. Proc Natl Acad Sci U S A. 2015 Feb 10; 112(6):E516-25. PMID: 25624474; PMCID: PMC4330758.
    71. Lindert S, Cheng Y, Kekenes-Huskey P, Regnier M, McCammon JA. Effects of HCM cTnI mutation R145G on troponin structure and modulation by PKA phosphorylation elucidated by molecular dynamics simulations. Biophys J. 2015 Jan 20; 108(2):395-407. PMID: 25606687; PMCID: PMC4302190.
    72. Wang N, Zhou S, Kekenes-Huskey PM, Li B, McCammon JA. Poisson-Boltzmann versus Size-Modified Poisson-Boltzmann Electrostatics Applied to Lipid Bilayers. J Phys Chem B. 2014 Dec 26; 118(51):14827-32. PMID: 25426875; PMCID: PMC4280115.
    73. Kim MO, Feng X, Feixas F, Zhu W, Lindert S, Bogue S, Sinko W, de Oliveira C, Rao G, Oldfield E, McCammon JA. A Molecular Dynamics Investigation of Mycobacterium tuberculosis Prenyl Synthases: Conformational Flexibility and Implications for Computer-aided Drug Discovery. Chem Biol Drug Des. 2015 Jun; 85(6):756-69. PMID: 25352216; PMCID: PMC4412765.
    74. Metzger VT, Eun C, Kekenes-Huskey PM, Huber G, McCammon JA. Electrostatic channeling in P. falciparum DHFR-TS: Brownian dynamics and Smoluchowski modeling. Biophys J. 2014 Nov 18; 107(10):2394-402. PMID: 25418308; PMCID: PMC4241442.
    75. Bertolini R, Goepfert C, Andrieu T, Nichols S, Walter MA, Frey FJ, McCammon JA, Frey BM. 18F-RB390: innovative ligand for imaging the T877A androgen receptor mutant in prostate cancer via positron emission tomography (PET). Prostate. 2015 Mar 01; 75(4):348-59. PMID: 25358634.
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    76. Lindert S, Tallorin L, Nguyen QG, Burkart MD, McCammon JA. In silico screening for Plasmodium falciparum enoyl-ACP reductase inhibitors. J Comput Aided Mol Des. 2015 Jan; 29(1):79-87. PMID: 25344312; PMCID: PMC4278936.
    77. Cheng Y, Lindert S, Kekenes-Huskey P, Rao VS, Solaro RJ, Rosevear PR, Amaro R, McCulloch AD, McCammon JA, Regnier M. Computational studies of the effect of the S23D/S24D troponin I mutation on cardiac troponin structural dynamics. Biophys J. 2014 Oct 07; 107(7):1675-85. PMID: 25296321; PMCID: PMC4190606.
    78. Tallorin LC, Durrant JD, Nguyen QG, McCammon JA, Burkart MD. Celastrol inhibits Plasmodium falciparum enoyl-acyl carrier protein reductase. Bioorg Med Chem. 2014 Nov 01; 22(21):6053-6061. PMID: 25284249.
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    79. Rao V, Cheng Y, Lindert S, Wang D, Oxenford L, McCulloch AD, McCammon JA, Regnier M. PKA phosphorylation of cardiac troponin I modulates activation and relaxation kinetics of ventricular myofibrils. Biophys J. 2014 Sep 02; 107(5):1196-1204. PMID: 25185555; PMCID: PMC4156663.
    80. Brown LM, Rogers KE, Aroonsakool N, McCammon JA, Insel PA. Allosteric inhibition of Epac: computational modeling and experimental validation to identify allosteric sites and inhibitors. J Biol Chem. 2014 Oct 17; 289(42):29148-57. PMID: 25183009; PMCID: PMC4200268.
    81. Kim MO, Blachly PG, Kaus JW, McCammon JA. Protocols utilizing constant pH molecular dynamics to compute pH-dependent binding free energies. J Phys Chem B. 2015 Jan 22; 119(3):861-72. PMID: 25134690; PMCID: PMC4306499.
    82. Boechi L, Pierce L, Komives EA, McCammon JA. Trypsinogen activation as observed in accelerated molecular dynamics simulations. Protein Sci. 2014 Nov; 23(11):1550-8. PMID: 25131668; PMCID: PMC4241106.
    83. Martin DP, Blachly PG, McCammon JA, Cohen SM. Exploring the influence of the protein environment on metal-binding pharmacophores. J Med Chem. 2014 Aug 28; 57(16):7126-35. PMID: 25116076; PMCID: PMC4148168.
    84. Blachly PG, Sandala GM, Giammona DA, Liu T, Bashford D, McCammon JA, Noodleman L. Use of Broken-Symmetry Density Functional Theory To Characterize the IspH Oxidized State: Implications for IspH Mechanism and Inhibition. J Chem Theory Comput. 2014 Sep 09; 10(9):3871-3884. PMID: 25221444.
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    85. Lindert S, Li MX, Sykes BD, McCammon JA. Computer-aided drug discovery approach finds calcium sensitizer of cardiac troponin. Chem Biol Drug Des. 2015 Feb; 85(2):99-106. PMID: 24954187; PMCID: PMC4456024.
    86. McCammon JA, Roux B, Voth G, Yang W. Special Issue on Free Energy. J Chem Theory Comput. 2014 Jul 08; 10(7):2631. PMID: 26586502.
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    87. Sinko W, Wang Y, Zhu W, Zhang Y, Feixas F, Cox CL, Mitchell DA, Oldfield E, McCammon JA. Undecaprenyl diphosphate synthase inhibitors: antibacterial drug leads. J Med Chem. 2014 Jul 10; 57(13):5693-701. PMID: 24827744.
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    88. Liu YL, Lindert S, Zhu W, Wang K, McCammon JA, Oldfield E. Taxodione and arenarone inhibit farnesyl diphosphate synthase by binding to the isopentenyl diphosphate site. Proc Natl Acad Sci U S A. 2014 Jun 24; 111(25):E2530-9. PMID: 24927548; PMCID: PMC4078810.
    89. Eun C, Ortiz-Sánchez JM, Da L, Wang D, McCammon JA. Molecular dynamics simulation study of conformational changes of transcription factor TFIIS during RNA polymerase II transcriptional arrest and reactivation. PLoS One. 2014; 9(5):e97975. PMID: 24842057; PMCID: PMC4026522.
    90. Kekenes-Huskey PM, Gillette AK, McCammon JA. Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation. J Chem Phys. 2014 May 07; 140(17):174106. PMID: 24811624.
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    91. Kaus JW, Arrar M, McCammon JA. Accelerated adaptive integration method. J Phys Chem B. 2014 May 15; 118(19):5109-18. PMID: 24780083; PMCID: PMC4025579.
    92. Miao Y, Sinko W, Pierce L, Bucher D, Walker RC, McCammon JA. Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation. J Chem Theory Comput. 2014 Jul 08; 10(7):2677-2689. PMID: 25061441.
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    93. Martin DP, Blachly PG, Marts AR, Woodruff TM, de Oliveira CA, McCammon JA, Tierney DL, Cohen SM. 'Unconventional' coordination chemistry by metal chelating fragments in a metalloprotein active site. J Am Chem Soc. 2014 Apr 09; 136(14):5400-6. PMID: 24635441; PMCID: PMC4104174.
    94. Ivetac A, Swift SE, Boyer PL, Diaz A, Naughton J, Young JA, Hughes SH, McCammon JA. Discovery of novel inhibitors of HIV-1 reverse transcriptase through virtual screening of experimental and theoretical ensembles. Chem Biol Drug Des. 2014 May; 83(5):521-31. PMID: 24405985; PMCID: PMC3999242.
    95. Eun C, Kekenes-Huskey PM, Metzger VT, McCammon JA. A model study of sequential enzyme reactions and electrostatic channeling. J Chem Phys. 2014 Mar 14; 140(10):105101. PMID: 24628210; PMCID: PMC3977847.
    96. Götz AW, Bucher D, Lindert S, McCammon JA. Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields. J Chem Theory Comput. 2014 Apr 08; 10(4):1631-1637. PMID: 24803868.
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    97. Zhou S, Cheng LT, Dzubiella J, Li B, McCammon JA. Variational Implicit Solvation with Poisson-Boltzmann Theory. J Chem Theory Comput. 2014 Apr 08; 10(4):1454-1467. PMID: 24803864.
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    98. Jacobitz AW, Wereszczynski J, Yi SW, Amer BR, Huang GL, Nguyen AV, Sawaya MR, Jung ME, McCammon JA, Clubb RT. Structural and computational studies of the Staphylococcus aureus sortase B-substrate complex reveal a substrate-stabilized oxyanion hole. J Biol Chem. 2014 Mar 28; 289(13):8891-902. PMID: 24519933; PMCID: PMC3979406.
    99. Lindert S, Maslennikov I, Chiu EJ, Pierce LC, McCammon JA, Choe S. Drug screening strategy for human membrane proteins: from NMR protein backbone structure to in silica- and NMR-screened hits. Biochem Biophys Res Commun. 2014 Mar 21; 445(4):724-33. PMID: 24525125; PMCID: PMC4457379.
    100. Brown LM, Rogers KE, McCammon JA, Insel PA. Identification and validation of modulators of exchange protein activated by cAMP (Epac) activity: structure-function implications for Epac activation and inhibition. J Biol Chem. 2014 Mar 21; 289(12):8217-30. PMID: 24497631.
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    101. Guo Z, Li B, Dzubiella J, Cheng LT, McCammon JA, Che J. Heterogeneous Hydration of p53/MDM2 Complex. J Chem Theory Comput. 2014 Mar 11; 10(3):1302-1313. PMID: 24803860.
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    102. Miao Y, Nichols SE, McCammon JA. Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics. Phys Chem Chem Phys. 2014 Apr 14; 16(14):6398-406. PMID: 24445284.
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    103. Miller B, Friedman AJ, Choi H, Hogan J, McCammon JA, Hook V, Gerwick WH. The marine cyanobacterial metabolite gallinamide A is a potent and selective inhibitor of human cathepsin L. J Nat Prod. 2014 Jan 24; 77(1):92-9. PMID: 24364476; PMCID: PMC3932306.
    104. Nguyen C, Haushalter RW, Lee DJ, Markwick PR, Bruegger J, Caldara-Festin G, Finzel K, Jackson DR, Ishikawa F, O'Dowd B, McCammon JA, Opella SJ, Tsai SC, Burkart MD. Trapping the dynamic acyl carrier protein in fatty acid biosynthesis. Nature. 2014 Jan 16; 505(7483):427-31. PMID: 24362570; PMCID: PMC4437705.
    105. Blachly PG, de Oliveira CA, Williams SL, McCammon JA. Utilizing a dynamical description of IspH to aid in the development of novel antimicrobial drugs. PLoS Comput Biol. 2013; 9(12):e1003395. PMID: 24367248; PMCID: PMC3868525.
    106. Feixas F, Lindert S, Sinko W, McCammon JA. Exploring the role of receptor flexibility in structure-based drug discovery. Biophys Chem. 2014 Feb; 186:31-45. PMID: 24332165; PMCID: PMC4459653.
    107. Kekenes-Huskey PM, Liao T, Gillette AK, Hake JE, Zhang Y, Michailova AP, McCulloch AD, McCammon JA. Molecular and subcellular-scale modeling of nucleotide diffusion in the cardiac myofilament lattice. Biophys J. 2013 Nov 05; 105(9):2130-40. PMID: 24209858; PMCID: PMC3835335.
    108. Miao Y, Nichols SE, McCammon JA. Mapping of allosteric druggable sites in activation-associated conformers of the M2 muscarinic receptor. Chem Biol Drug Des. 2014 Feb; 83(2):237-46. PMID: 24112716; PMCID: PMC4012891.
    109. Lindert S, Bucher D, Eastman P, Pande V, McCammon JA. Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units. J Chem Theory Comput. 2013 Nov 12; 9(11):4684-4691. PMID: 24634618.
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    110. Chan AH, Wereszczynski J, Amer BR, Yi SW, Jung ME, McCammon JA, Clubb RT. Discovery of Staphylococcus aureus sortase A inhibitors using virtual screening and the relaxed complex scheme. Chem Biol Drug Des. 2013 Oct; 82(4):418-28. PMID: 23701677; PMCID: PMC3841297.
    111. Boechi L, de Oliveira CA, Da Fonseca I, Kizjakina K, Sobrado P, Tanner JJ, McCammon JA. Substrate-dependent dynamics of UDP-galactopyranose mutase: Implications for drug design. Protein Sci. 2013 Nov; 22(11):1490-501. PMID: 23934860.
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    112. Arrar M, de Oliveira CA, McCammon JA. Inactivating mutation in histone deacetylase 3 stabilizes its active conformation. Protein Sci. 2013 Oct; 22(10):1306-12. PMID: 23904210; PMCID: PMC3795489.
    113. Tikhonova IG, Selvam B, Ivetac A, Wereszczynski J, McCammon JA. Simulations of biased agonists in the ß(2) adrenergic receptor with accelerated molecular dynamics. Biochemistry. 2013 Aug 20; 52(33):5593-603. PMID: 23879802.
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    114. Zhou S, Rogers KE, de Oliveira CA, Baron R, Cheng LT, Dzubiella J, Li B, McCammon JA. Variational Implicit-Solvent Modeling of Host-Guest Binding: A Case Study on Cucurbit[7]uril| J Chem Theory Comput. 2013 Sep 10; 9(9):4195-4204. PMID: 24039554.
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    115. Eun C, Kekenes-Huskey PM, McCammon JA. Influence of neighboring reactive particles on diffusion-limited reactions. J Chem Phys. 2013 Jul 28; 139(4):044117. PMID: 23901970; PMCID: PMC3745503.
    116. Bucher D, Hsu YH, Mouchlis VD, Dennis EA, McCammon JA. Insertion of the Ca²?-independent phospholipase A2 into a phospholipid bilayer via coarse-grained and atomistic molecular dynamics simulations. PLoS Comput Biol. 2013; 9(7):e1003156. PMID: 23935474; PMCID: PMC3723492.
    117. Zhao Y, Kwan YY, Che J, Li B, McCammon JA. Phase-field approach to implicit solvation of biomolecules with Coulomb-field approximation. J Chem Phys. 2013 Jul 14; 139(2):024111. PMID: 23862933; PMCID: PMC3724799.
    118. Sinko W, Miao Y, de Oliveira CA, McCammon JA. Population based reweighting of scaled molecular dynamics. J Phys Chem B. 2013 Oct 24; 117(42):12759-68. PMID: 23721224; PMCID: PMC3808002.
    119. Durrant JD, Friedman AJ, Rogers KE, McCammon JA. Comparing neural-network scoring functions and the state of the art: applications to common library screening. J Chem Inf Model. 2013 Jul 22; 53(7):1726-35. PMID: 23734946; PMCID: PMC3735370.
    120. Lindert S, Meiler J, McCammon JA. Iterative Molecular Dynamics-Rosetta Protein Structure Refinement Protocol to Improve Model Quality. J Chem Theory Comput. 2013 Aug 13; 9(8):3843-3847. PMID: 23956701.
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    121. Liao T, Zhang Y, Kekenes-Huskey PM, Cheng Y, Michailova A, McCulloch AD, Holst M, McCammon JA. Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes. Mol Based Math Biol. 2013 Jul; 1. PMID: 24352481.
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    122. Miao Y, Nichols SE, Gasper PM, Metzger VT, McCammon JA. Activation and dynamic network of the M2 muscarinic receptor. Proc Natl Acad Sci U S A. 2013 Jul 02; 110(27):10982-7. PMID: 23781107; PMCID: PMC3703993.
    123. Lindert S, Zhu W, Liu YL, Pang R, Oldfield E, McCammon JA. Farnesyl diphosphate synthase inhibitors from in silico screening. Chem Biol Drug Des. 2013 Jun; 81(6):742-8. PMID: 23421555; PMCID: PMC3671582.
    124. Fuglestad B, Gasper PM, McCammon JA, Markwick PR, Komives EA. Correlated motions and residual frustration in thrombin. J Phys Chem B. 2013 Oct 24; 117(42):12857-63. PMID: 23621631; PMCID: PMC3808083.
    125. Wang N, Huber GA, McCammon JA. Assessing the two-body diffusion tensor calculated by the bead models. J Chem Phys. 2013 May 28; 138(20):204117. PMID: 23742464; PMCID: PMC3683057.
    126. Durrant JD, Lindert S, McCammon JA. AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design. J Mol Graph Model. 2013 Jul; 44:104-12. PMID: 23792207; PMCID: PMC3842281.
    127. Nichols SE, Hernández CX, Wang Y, McCammon JA. Structure-based network analysis of an evolved G protein-coupled receptor homodimer interface. Protein Sci. 2013 Jun; 22(6):745-54. PMID: 23553730; PMCID: PMC3690714.
    128. Kim MO, Nichols SE, Wang Y, McCammon JA. Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC. J Comput Aided Mol Des. 2013 Mar; 27(3):235-46. PMID: 23579613; PMCID: PMC3639364.
    129. Baron R, McCammon JA. Molecular recognition and ligand association. Annu Rev Phys Chem. 2013; 64:151-75. PMID: 23473376.
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    130. Guerry P, Salmon L, Mollica L, Ortega Roldan JL, Markwick P, van Nuland NA, McCammon JA, Blackledge M. Mapping the population of protein conformational energy sub-states from NMR dipolar couplings. Angew Chem Int Ed Engl. 2013 Mar 11; 52(11):3181-5. PMID: 23371543.
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    131. Guo Z, Li B, Dzubiella J, Cheng LT, McCammon JA, Che J. Evaluation of Hydration Free Energy by Level-Set Variational Implicit-Solvent Model with Coulomb-Field Approximation. J Chem Theory Comput. 2013 Mar 12; 9(3):1778-1787. PMID: 23505345.
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    132. Hsu YH, Bucher D, Cao J, Li S, Yang SW, Kokotos G, Woods VL, McCammon JA, Dennis EA. Fluoroketone inhibition of Ca(2+)-independent phospholipase A2 through binding pocket association defined by hydrogen/deuterium exchange and molecular dynamics. J Am Chem Soc. 2013 Jan 30; 135(4):1330-7. PMID: 23256506; PMCID: PMC3561773.
    133. Setny P, Baron R, Michael Kekenes-Huskey P, McCammon JA, Dzubiella J. Solvent fluctuations in hydrophobic cavity-ligand binding kinetics. Proc Natl Acad Sci U S A. 2013 Jan 22; 110(4):1197-202. PMID: 23297241; PMCID: PMC3557044.
    134. Sinko W, Lindert S, McCammon JA. Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design. Chem Biol Drug Des. 2013 Jan; 81(1):41-9. PMID: 23253130; PMCID: PMC3540989.
    135. Zhu W, Zhang Y, Sinko W, Hensler ME, Olson J, Molohon KJ, Lindert S, Cao R, Li K, Wang K, Wang Y, Liu YL, Sankovsky A, de Oliveira CA, Mitchell DA, Nizet V, McCammon JA, Oldfield E. Antibacterial drug leads targeting isoprenoid biosynthesis. Proc Natl Acad Sci U S A. 2013 Jan 02; 110(1):123-8. PMID: 23248302; PMCID: PMC3538244.
    136. Arrar M, de Oliveira CA, Fajer M, Sinko W, McCammon JA. w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations. J Chem Theory Comput. 2013 Jan 08; 9(1):18-23. PMID: 23316122.
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    137. Kappel K, Wereszczynski J, Clubb RT, McCammon JA. The binding mechanism, multiple binding modes, and allosteric regulation of Staphylococcus aureus Sortase A probed by molecular dynamics simulations. Protein Sci. 2012 Dec; 21(12):1858-71. PMID: 23023444; PMCID: PMC3575916.
    138. Arrar M, Turnham R, Pierce L, de Oliveira CA, McCammon JA. Structural insight into the separate roles of inositol tetraphosphate and deacetylase-activating domain in activation of histone deacetylase 3. Protein Sci. 2013 Jan; 22(1):83-92. PMID: 23139175; PMCID: PMC3575863.
    139. Kekenes-Huskey PM, Lindert S, McCammon JA. Molecular basis of calcium-sensitizing and desensitizing mutations of the human cardiac troponin C regulatory domain: a multi-scale simulation study. PLoS Comput Biol. 2012; 8(11):e1002777. PMID: 23209387; PMCID: PMC3510055.
    140. Gasper PM, Fuglestad B, Komives EA, Markwick PR, McCammon JA. Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities. Proc Natl Acad Sci U S A. 2012 Dec 26; 109(52):21216-22. PMID: 23197839; PMCID: PMC3535651.
    141. Kekenes-Huskey PM, Gillette A, Hake J, McCammon JA. Finite Element Estimation of Protein-Ligand Association Rates with Post-Encounter Effects: Applications to Calcium binding in Troponin C and SERCA. Comput Sci Discov. 2012 Oct 31; 5. PMID: 23293662.
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    142. Rogers KE, Ortiz-Sánchez JM, Baron R, Fajer M, de Oliveira CA, McCammon JA. On the Role of Dewetting Transitions in Host-Guest Binding Free Energy Calculations. J Chem Theory Comput. 2013 Jan 08; 9(1):46-53. PMID: 23316123.
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    143. Lindert S, Kekenes-Huskey PM, McCammon JA. Long-timescale molecular dynamics simulations elucidate the dynamics and kinetics of exposure of the hydrophobic patch in troponin C. Biophys J. 2012 Oct 17; 103(8):1784-9. PMID: 23083722; PMCID: PMC3475331.
    144. Lindert S, McCammon JA. Dynamics of Plasmodium falciparum enoyl-ACP reductase and implications on drug discovery. Protein Sci. 2012 Nov; 21(11):1734-45. PMID: 22969045; PMCID: PMC3527710.
    145. Kekenes-Huskey PM, Cheng Y, Hake JE, Sachse FB, Bridge JH, Holst MJ, McCammon JA, McCulloch AD, Michailova AP. Modeling effects of L-type ca(2+) current and na(+)-ca(2+) exchanger on ca(2+) trigger flux in rabbit myocytes with realistic T-tubule geometries. Front Physiol. 2012; 3:351. PMID: 23060801; PMCID: PMC3463892.
    146. Schlamadinger DE, Wang Y, McCammon JA, Kim JE. Spectroscopic and computational study of melittin, cecropin A, and the hybrid peptide CM15. J Phys Chem B. 2012 Sep 06; 116(35):10600-8. PMID: 22845179.
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    147. Pierce LC, Salomon-Ferrer R, Augusto F de Oliveira C, McCammon JA, Walker RC. Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics. J Chem Theory Comput. 2012 Sep 11; 8(9):2997-3002. PMID: 22984356.
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    148. Konecny R, Baker NA, McCammon JA. iAPBS: a programming interface to Adaptive Poisson-Boltzmann Solver (APBS). Comput Sci Discov. 2012 Jul 26; 5(1). PMID: 22905037.
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    149. Ortiz-Sanchez JM, Nichols SE, Sayyah J, Brown JH, McCammon JA, Grant BJ. Identification of potential small molecule binding pockets on Rho family GTPases. PLoS One. 2012; 7(7):e40809. PMID: 22815826; PMCID: PMC3397943.
    150. Fuglestad B, Gasper PM, Tonelli M, McCammon JA, Markwick PR, Komives EA. The dynamic structure of thrombin in solution. Biophys J. 2012 Jul 03; 103(1):79-88. PMID: 22828334; PMCID: PMC3388214.
    151. Ortiz-Sánchez JM, Bucher D, Pierce LC, Markwick PR, McCammon JA. Exploring the Photophysical Properties of Molecular Systems Using Excited State Accelerated ab Initio Molecular Dynamics. J Chem Theory Comput. 2012 Aug 14; 8(8):2752-2761. PMID: 22904696.
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    152. Lindert S, Durrant JD, McCammon JA. LigMerge: a fast algorithm to generate models of novel potential ligands from sets of known binders. Chem Biol Drug Des. 2012 Sep; 80(3):358-65. PMID: 22594624; PMCID: PMC3462068.
    153. Rogers KE, Keränen H, Durrant JD, Ratnam J, Doak A, Arkin MR, McCammon JA. Novel cruzain inhibitors for the treatment of Chagas' disease. Chem Biol Drug Des. 2012 Sep; 80(3):398-405. PMID: 22613098; PMCID: PMC3503458.
    154. Salmon L, Pierce L, Grimm A, Ortega Roldan JL, Mollica L, Jensen MR, van Nuland N, Markwick PR, McCammon JA, Blackledge M. Multi-timescale conformational dynamics of the SH3 domain of CD2-associated protein using NMR spectroscopy and accelerated molecular dynamics. Angew Chem Int Ed Engl. 2012 Jun 18; 51(25):6103-6. PMID: 22565613; PMCID: PMC3541011.
    155. Friedman AJ, Durrant JD, Pierce LC, McCorvie TJ, Timson DJ, McCammon JA. The molecular dynamics of Trypanosoma brucei UDP-galactose 4'-epimerase: a drug target for African sleeping sickness. Chem Biol Drug Des. 2012 Aug; 80(2):173-81. PMID: 22487100; PMCID: PMC3399956.
    156. Wereszczynski J, McCammon JA. Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations. Proc Natl Acad Sci U S A. 2012 May 15; 109(20):7759-64. PMID: 22547793; PMCID: PMC3356667.
    157. Bauler P, Huber GA, McCammon JA. Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions. J Chem Phys. 2012 Apr 28; 136(16):164107. PMID: 22559470; PMCID: PMC3350536.
    158. Hake J, Edwards AG, Yu Z, Kekenes-Huskey PM, Michailova AP, McCammon JA, Holst MJ, Hoshijima M, McCulloch AD. Modelling cardiac calcium sparks in a three-dimensional reconstruction of a calcium release unit. J Physiol. 2012 Sep 15; 590(18):4403-22. PMID: 22495592.
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    159. Durrant JD, McCammon JA. AutoClickChem: click chemistry in silico. PLoS Comput Biol. 2012; 8(3):e1002397. PMID: 22438795; PMCID: PMC3305364.
    160. Wereszczynski J, McCammon JA. Simulations of the p97 complex suggest novel conformational states of hydrolysis intermediates. Protein Sci. 2012 Apr; 21(4):475-86. PMID: 22238181; PMCID: PMC3375748.
    161. Wang Y, Schlamadinger DE, Kim JE, McCammon JA. Comparative molecular dynamics simulations of the antimicrobial peptide CM15 in model lipid bilayers. Biochim Biophys Acta. 2012 May; 1818(5):1402-9. PMID: 22387432; PMCID: PMC3329965.
    162. Lawrenz M, Wereszczynski J, Ortiz-Sánchez JM, Nichols SE, McCammon JA. Thermodynamic integration to predict host-guest binding affinities. J Comput Aided Mol Des. 2012 May; 26(5):569-76. PMID: 22350568; PMCID: PMC4113475.
    163. Lindert S, Kekenes-Huskey PM, Huber G, Pierce L, McCammon JA. Dynamics and calcium association to the N-terminal regulatory domain of human cardiac troponin C: a multiscale computational study. J Phys Chem B. 2012 Jul 26; 116(29):8449-59. PMID: 22329450; PMCID: PMC3405770.
    164. Holst M, McCammon JA, Yu Z, Zhou Y, Zhu Y. ADAPTIVE FINITE ELEMENT MODELING TECHNIQUES FOR THE POISSON-BOLTZMANN EQUATION. Commun Comput Phys. 2012; 11(1):179-214. PMID: 21949541.
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    165. Ivetac A, McCammon JA. A molecular dynamics ensemble-based approach for the mapping of druggable binding sites. Methods Mol Biol. 2012; 819:3-12. PMID: 22183526.
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    166. Lawrenz M, Baron R, Wang Y, McCammon JA. Independent-Trajectory Thermodynamic Integration: a practical guide to protein-drug binding free energy calculations using distributed computing. Methods Mol Biol. 2012; 819:469-86. PMID: 22183552.
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    167. Nichols SE, Baron R, McCammon JA. On the use of molecular dynamics receptor conformations for virtual screening. Methods Mol Biol. 2012; 819:93-103. PMID: 22183532.
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    168. Sinko W, Sierecki E, de Oliveira CA, McCammon JA. Guide to virtual screening: application to the Akt phosphatase PHLPP. Methods Mol Biol. 2012; 819:561-73. PMID: 22183558.
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    169. Wereszczynski J, McCammon JA. Accelerated molecular dynamics in computational drug design. Methods Mol Biol. 2012; 819:515-24. PMID: 22183555.
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    170. Wang Z, Che J, Cheng LT, Dzubiella J, Li B, McCammon JA. Level-Set Variational Implicit-Solvent Modeling of Biomolecules with the Coulomb-Field Approximation. J Chem Theory Comput. 2012 Feb 14; 8(2):386-397. PMID: 22346739.
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    171. Grant BJ, Gheorghe DM, Zheng W, Alonso M, Huber G, Dlugosz M, McCammon JA, Cross RA. Electrostatically biased binding of kinesin to microtubules. PLoS Biol. 2011 Nov; 9(11):e1001207. PMID: 22140358; PMCID: PMC3226556.
    172. Sinko W, de Oliveira CA, Pierce LC, McCammon JA. Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations. J Chem Theory Comput. 2012 Jan 10; 8(1):17-23. PMID: 22241967.
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    173. Wereszczynski J, McCammon JA. Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition. Q Rev Biophys. 2012 Feb; 45(1):1-25. PMID: 22082669; PMCID: PMC3291752.
    174. Bucher D, Grant BJ, McCammon JA. Induced fit or conformational selection? The role of the semi-closed state in the maltose binding protein. Biochemistry. 2011 Dec 06; 50(48):10530-9. PMID: 22050600; PMCID: PMC3226325.
    175. Durrant JD, McCammon JA. NNScore 2.0: a neural-network receptor-ligand scoring function. J Chem Inf Model. 2011 Nov 28; 51(11):2897-903. PMID: 22017367.
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    176. Durrant JD, McCammon JA. Molecular dynamics simulations and drug discovery. BMC Biol. 2011 Oct 28; 9:71. PMID: 22035460.
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    177. Grant BJ, Lukman S, Hocker HJ, Sayyah J, Brown JH, McCammon JA, Gorfe AA. Novel allosteric sites on Ras for lead generation. PLoS One. 2011; 6(10):e25711. PMID: 22046245; PMCID: PMC3201956.
    178. Markwick PR, McCammon JA. Studying functional dynamics in bio-molecules using accelerated molecular dynamics. Phys Chem Chem Phys. 2011 Dec 07; 13(45):20053-65. PMID: 22015376.
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    179. de Oliveira CA, Grant BJ, Zhou M, McCammon JA. Large-scale conformational changes of Trypanosoma cruzi proline racemase predicted by accelerated molecular dynamics simulation. PLoS Comput Biol. 2011 Oct; 7(10):e1002178. PMID: 22022240; PMCID: PMC3192803.
    180. Durrant JD, Friedman AJ, McCammon JA. CrystalDock: a novel approach to fragment-based drug design. J Chem Inf Model. 2011 Oct 24; 51(10):2573-80. PMID: 21910501.
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    181. Williams SL, Blachly PG, McCammon JA. Measuring the successes and deficiencies of constant pH molecular dynamics: a blind prediction study. Proteins. 2011 Dec; 79(12):3381-8. PMID: 22072520.
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    182. Durrant JD, McCammon JA. Towards the development of novel Trypanosoma brucei RNA editing ligase 1 inhibitors. BMC Pharmacol. 2011 Aug 30; 11:9. PMID: 21878090.
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    183. Wang Y, Markwick PR, de Oliveira CA, McCammon JA. Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics. J Chem Theory Comput. 2011 Oct 11; 7(10):3199-3207. PMID: 22003320.
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    184. Durrant JD, McCammon JA. HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis. J Mol Graph Model. 2011 Nov; 31:5-9. PMID: 21880522.
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    185. Durrant JD, Cao R, Gorfe AA, Zhu W, Li J, Sankovsky A, Oldfield E, McCammon JA. Non-bisphosphonate inhibitors of isoprenoid biosynthesis identified via computer-aided drug design. Chem Biol Drug Des. 2011 Sep; 78(3):323-32. PMID: 21696546; PMCID: PMC3155669.
    186. Romanowska J, McCammon JA, Trylska J. Understanding the origins of bacterial resistance to aminoglycosides through molecular dynamics mutational study of the ribosomal A-site. PLoS Comput Biol. 2011 Jul; 7(7):e1002099. PMID: 21814503.
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    187. Durrant JD, de Oliveira CA, McCammon JA. Pyrone-based inhibitors of metalloproteinase types 2 and 3 may work as conformation-selective inhibitors. Chem Biol Drug Des. 2011 Aug; 78(2):191-8. PMID: 21609408.
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    188. Lawrenz M, Baron R, Wang Y, McCammon JA. Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies. J Chem Theory Comput. 2011 Jun 02; 7(7):2224-2232. PMID: 21811708.
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    189. Nichols SE, Baron R, Ivetac A, McCammon JA. Predictive power of molecular dynamics receptor structures in virtual screening. J Chem Inf Model. 2011 Jun 27; 51(6):1439-46. PMID: 21534609.
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    190. Pierce LC, Markwick PR, McCammon JA, Doltsinis NL. Accelerating chemical reactions: exploring reactive free-energy surfaces using accelerated ab initio molecular dynamics. J Chem Phys. 2011 May 07; 134(17):174107. PMID: 21548673.
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    191. Bucher D, Grant BJ, Markwick PR, McCammon JA. Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics. PLoS Comput Biol. 2011 Apr; 7(4):e1002034. PMID: 21533070; PMCID: PMC3080849.
    192. Sinko W, de Oliveira C, Williams S, Van Wynsberghe A, Durrant JD, Cao R, Oldfield E, McCammon JA. Applying molecular dynamics simulations to identify rarely sampled ligand-bound conformational states of undecaprenyl pyrophosphate synthase, an antibacterial target. Chem Biol Drug Des. 2011 Jun; 77(6):412-20. PMID: 21294851.
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    193. Dlugosz M, Huber GA, McCammon JA, Trylska J. Brownian dynamics study of the association between the 70S ribosome and elongation factor G. Biopolymers. 2011 Sep; 95(9):616-27. PMID: 21394717; PMCID: PMC3125448.
    194. Skjaerven L, Grant B, Muga A, Teigen K, McCammon JA, Reuter N, Martinez A. Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations. PLoS Comput Biol. 2011 Mar; 7(3):e1002004. PMID: 21423709; PMCID: PMC3053311.
    195. Bucher D, Pierce LC, McCammon JA, Markwick PR. On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations. J Chem Theory Comput. 2011 Apr 12; 7(4):890-897. PMID: 21494425.
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    196. Mereghetti P, Kokh D, McCammon JA, Wade RC. Diffusion and association processes in biological systems: theory, computation and experiment. BMC Biophys. 2011 Mar 02; 4:2. PMID: 21595997.
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    197. McCammon JA. Gated Diffusion-controlled Reactions. BMC Biophys. 2011 Mar 02; 4:4. PMID: 21595999; PMCID: PMC3093672.
    198. Sander T, Frølund B, Bruun AT, Ivanov I, McCammon JA, Balle T. New insights into the GABA(A) receptor structure and orthosteric ligand binding: receptor modeling guided by experimental data. Proteins. 2011 May; 79(5):1458-77. PMID: 21365676; PMCID: PMC3076690.
    199. Baron R, Binda C, Tortorici M, McCammon JA, Mattevi A. Molecular mimicry and ligand recognition in binding and catalysis by the histone demethylase LSD1-CoREST complex. Structure. 2011 Feb 09; 19(2):212-20. PMID: 21300290.
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    200. Williams SL, de Oliveira CA, Vazquez H, McCammon JA. From Zn to Mn: the study of novel manganese-binding groups in the search for new drugs against tuberculosis. Chem Biol Drug Des. 2011 Feb; 77(2):117-23. PMID: 21266015.
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    201. Durrant JD, McCammon JA. BINANA: a novel algorithm for ligand-binding characterization. J Mol Graph Model. 2011 Apr; 29(6):888-93. PMID: 21310640.
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    202. Markwick PR, Pierce LC, Goodin DB, McCammon JA. Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam. J Phys Chem Lett. 2011 Feb 03; 2(3):158-164. PMID: 21307966.
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    203. Wang Y, Harrison CB, Schulten K, McCammon JA. Implementation of Accelerated Molecular Dynamics in NAMD. Comput Sci Discov. 2011; 4(1). PMID: 21686063.
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    204. Ivetac A, McCammon JA. Molecular recognition in the case of flexible targets. Curr Pharm Des. 2011; 17(17):1663-71. PMID: 21619526.
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    205. Grant BJ, McCammon JA, Gorfe AA. Conformational selection in G-proteins: lessons from Ras and Rho. Biophys J. 2010 Dec 01; 99(11):L87-9. PMID: 21112273; PMCID: PMC2998626.
    206. Durrant JD, de Oliveira CA, McCammon JA. POVME: an algorithm for measuring binding-pocket volumes. J Mol Graph Model. 2011 Feb; 29(5):773-6. PMID: 21147010.
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    207. Huber GA, McCammon JA. Browndye: A Software Package for Brownian Dynamics. Comput Phys Commun. 2010 Nov 01; 181(11):1896-1905. PMID: 21132109.
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    208. Peng LX, Ivetac A, Chaudhari AS, Van S, Zhao G, Yu L, Howell SB, McCammon JA, Gough DA. Characterization of a clinical polymer-drug conjugate using multiscale modeling. Biopolymers. 2010 Nov; 93(11):936-51. PMID: 20564048; PMCID: PMC3099131.
    209. Cheng Y, Yu Z, Hoshijima M, Holst MJ, McCulloch AD, McCammon JA, Michailova AP. Numerical analysis of Ca2+ signaling in rat ventricular myocytes with realistic transverse-axial tubular geometry and inhibited sarcoplasmic reticulum. PLoS Comput Biol. 2010 Oct 28; 6(10):e1000972. PMID: 21060856; PMCID: PMC2965743.
    210. Durrant JD, McCammon JA. NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexes. J Chem Inf Model. 2010 Oct 25; 50(10):1865-71. PMID: 20845954.
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    211. Sierecki E, Sinko W, McCammon JA, Newton AC. Discovery of small molecule inhibitors of the PH domain leucine-rich repeat protein phosphatase (PHLPP) by chemical and virtual screening. J Med Chem. 2010 Oct 14; 53(19):6899-911. PMID: 20836557; PMCID: PMC2951065.
    212. Wereszczynski J, McCammon JA. Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations. J Chem Theory Comput. 2010 Nov 09; 6(11):3285-3292. PMID: 21072329.
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    213. Durrant JD, McCammon JA. Computer-aided drug-discovery techniques that account for receptor flexibility. Curr Opin Pharmacol. 2010 Dec; 10(6):770-4. PMID: 20888294.
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    214. Lu B, Holst MJ, McCammon JA, Zhou YC. Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions. J Comput Phys. 2010 Sep 20; 229(19):6979-6994. PMID: 21709855.
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    215. Lukman S, Grant BJ, Gorfe AA, Grant GH, McCammon JA. The distinct conformational dynamics of K-Ras and H-Ras A59G. PLoS Comput Biol. 2010 Sep 09; 6(9). PMID: 20838576; PMCID: PMC2936511.
    216. Baron R, Setny P, McCammon JA. Water in cavity-ligand recognition. J Am Chem Soc. 2010 Sep 01; 132(34):12091-7. PMID: 20695475.
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    217. Radford RJ, Lawrenz M, Nguyen PC, McCammon JA, Tezcan FA. Porous protein frameworks with unsaturated metal centers in sterically encumbered coordination sites. Chem Commun (Camb). 2011 Jan 07; 47(1):313-5. PMID: 20740227.
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    218. Setny P, Baron R, McCammon JA. How Can Hydrophobic Association Be Enthalpy Driven? J Chem Theory Comput. 2010 Sep 14; 6(9):2866-2871. PMID: 20844599.
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    219. Lawrenz M, Wereszczynski J, Amaro R, Walker R, Roitberg A, McCammon JA. Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy. Proteins. 2010 Aug 15; 78(11):2523-32. PMID: 20602360; PMCID: PMC2902668.
    220. Ishizuka R, Huber GA, McCammon JA. Solvation Effect on the Conformations of Alanine Dipeptide: Integral Equation Approach. J Phys Chem Lett. 2010 Aug 05; 1(15):2279-2283. PMID: 20694049.
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    221. Durrant JD, Urbaniak MD, Ferguson MA, McCammon JA. Computer-aided identification of Trypanosoma brucei uridine diphosphate galactose 4'-epimerase inhibitors: toward the development of novel therapies for African sleeping sickness. J Med Chem. 2010 Jul 08; 53(13):5025-32. PMID: 20527952.
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    222. Ivetac A, McCammon JA. Mapping the druggable allosteric space of G-protein coupled receptors: a fragment-based molecular dynamics approach. Chem Biol Drug Des. 2010 Sep 01; 76(3):201-17. PMID: 20626410.
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    223. Rouffet M, de Oliveira CA, Udi Y, Agrawal A, Sagi I, McCammon JA, Cohen SM. From sensors to silencers: quinoline- and benzimidazole-sulfonamides as inhibitors for zinc proteases. J Am Chem Soc. 2010 Jun 23; 132(24):8232-3. PMID: 20507095; PMCID: PMC2886603.
    224. Tainer JA, McCammon JA, Ivanov I. Recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading. J Am Chem Soc. 2010 Jun 02; 132(21):7372-8. PMID: 20455582.
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    225. Lu B, Cheng X, Huang J, McCammon JA. AFMPB: An Adaptive Fast Multipole Poisson-Boltzmann Solver for Calculating Electrostatics in Biomolecular Systems. Comput Phys Commun. 2010 Jun 01; 181(6):1150-1160. PMID: 20532187.
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    226. Durrant JD, Keränen H, Wilson BA, McCammon JA. Computational identification of uncharacterized cruzain binding sites. PLoS Negl Trop Dis. 2010 May 11; 4(5):e676. PMID: 20485483.
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    227. Bauler P, Huber G, Leyh T, McCammon JA. Channeling by Proximity: The Catalytic Advantages of Active Site Colocalization Using Brownian Dynamics. J Phys Chem Lett. 2010 May 06; 1(9):1332-1335. PMID: 20454551.
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    228. Durrant JD, McCammon JA. Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug design. Comput Biol Chem. 2010 Apr; 34(2):97-105. PMID: 20427241.
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    229. Li B, Lu B, Wang Z, McCammon JA. Solutions to a reduced Poisson-Nernst-Planck system and determination of reaction rates. Physica A. 2010 Apr 01; 389(7):1329-1345. PMID: 20228879.
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    230. Sung JC, Van Wynsberghe AW, Amaro RE, Li WW, McCammon JA. Role of secondary sialic acid binding sites in influenza N1 neuraminidase. J Am Chem Soc. 2010 Mar 10; 132(9):2883-5. PMID: 20155919; PMCID: PMC2835425.
    231. Durrant JD, de Oliveira CA, McCammon JA. Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitors. J Mol Recognit. 2010 Mar-Apr; 23(2):173-82. PMID: 19882751.
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    232. Markwick PR, Cervantes CF, Abel BL, Komives EA, Blackledge M, McCammon JA. Enhanced conformational space sampling improves the prediction of chemical shifts in proteins. J Am Chem Soc. 2010 Feb 03; 132(4):1220-1. PMID: 20063881; PMCID: PMC2812018.
    233. Perryman AL, Forli S, Morris GM, Burt C, Cheng Y, Palmer MJ, Whitby K, McCammon JA, Phillips C, Olson AJ. A dynamic model of HIV integrase inhibition and drug resistance. J Mol Biol. 2010 Mar 26; 397(2):600-15. PMID: 20096702.
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    234. Durrant JD, Amaro RE, Xie L, Urbaniak MD, Ferguson MA, Haapalainen A, Chen Z, Di Guilmi AM, Wunder F, Bourne PE, McCammon JA. A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. PLoS Comput Biol. 2010 Jan 22; 6(1):e1000648. PMID: 20098496; PMCID: PMC2799658.
    235. Williams SL, de Oliveira CA, McCammon JA. Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics. J Chem Theory Comput. 2010 Feb 09; 6(2):560-568. PMID: 20148176.
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    236. Grant BJ, Gorfe AA, McCammon JA. Large conformational changes in proteins: signaling and other functions. Curr Opin Struct Biol. 2010 Apr; 20(2):142-7. PMID: 20060708; PMCID: PMC2866511.
    237. Khavrutskii IV, Grant B, Taylor SS, McCammon JA. A transition path ensemble study reveals a linchpin role for Mg(2+) during rate-limiting ADP release from protein kinase A. Biochemistry. 2009 Dec 08; 48(48):11532-45. PMID: 19886670.
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    238. Baron R, Hünenberger PH, McCammon JA. Absolute Single-Molecule Entropies from Quasi-Harmonic Analysis of Microsecond Molecular Dynamics: Correction Terms and Convergence Properties. J Chem Theory Comput. 2009 Dec 08; 5(12):3150-3160. PMID: 20011626.
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    239. Newhouse EI, Xu D, Markwick PR, Amaro RE, Pao HC, Wu KJ, Alam M, McCammon JA, Li WW. Mechanism of glycan receptor recognition and specificity switch for avian, swine, and human adapted influenza virus hemagglutinins: a molecular dynamics perspective. J Am Chem Soc. 2009 Dec 02; 131(47):17430-42. PMID: 19891427.
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    240. Markwick PR, Bouvignies G, Salmon L, McCammon JA, Nilges M, Blackledge M. Toward a unified representation of protein structural dynamics in solution. J Am Chem Soc. 2009 Nov 25; 131(46):16968-75. PMID: 19919148.
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    241. Sivendran S, Jones V, Sun D, Wang Y, Grzegorzewicz AE, Scherman MS, Napper AD, McCammon JA, Lee RE, Diamond SL, McNeil M. Identification of triazinoindol-benzimidazolones as nanomolar inhibitors of the Mycobacterium tuberculosis enzyme TDP-6-deoxy-d-xylo-4-hexopyranosid-4-ulose 3,5-epimerase (RmlC). Bioorg Med Chem. 2010 Jan 15; 18(2):896-908. PMID: 19969466.
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    242. Zhou HX, McCammon JA. The gates of ion channels and enzymes. Trends Biochem Sci. 2010 Mar; 35(3):179-85. PMID: 19926290.
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    243. Baron R, McCammon JA, Mattevi A. The oxygen-binding vs. oxygen-consuming paradigm in biocatalysis: structural biology and biomolecular simulation. Curr Opin Struct Biol. 2009 Dec; 19(6):672-9. PMID: 19896366.
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    244. Setny P, Wang Z, Cheng LT, Li B, McCammon JA, Dzubiella J. Dewetting-controlled binding of ligands to hydrophobic pockets. Phys Rev Lett. 2009 Oct 30; 103(18):187801. PMID: 19905832.
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    245. Cheng LT, Wang Z, Setny P, Dzubiella J, Li B, McCammon JA. Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach. J Chem Phys. 2009 Oct 14; 131(14):144102. PMID: 19831428.
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    246. Cervantes CF, Markwick PR, Sue SC, McCammon JA, Dyson HJ, Komives EA. Functional dynamics of the folded ankyrin repeats of I kappa B alpha revealed by nuclear magnetic resonance. Biochemistry. 2009 Aug 25; 48(33):8023-31. PMID: 19591507; PMCID: PMC2728578.
    247. Knight JD, Hamelberg D, McCammon JA, Kothary R. The role of conserved water molecules in the catalytic domain of protein kinases. Proteins. 2009 Aug 15; 76(3):527-35. PMID: 19425109.
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    248. Gorfe AA, Lu B, Yu Z, McCammon JA. Enzymatic activity versus structural dynamics: the case of acetylcholinesterase tetramer. Biophys J. 2009 Aug 05; 97(3):897-905. PMID: 19651048.
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    249. Fajer M, Swift RV, McCammon JA. Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics. J Comput Chem. 2009 Aug; 30(11):1719-25. PMID: 19421994.
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    250. Burke JE, Babakhani A, Gorfe AA, Kokotos G, Li S, Woods VL, McCammon JA, Dennis EA. Location of inhibitors bound to group IVA phospholipase A2 determined by molecular dynamics and deuterium exchange mass spectrometry. J Am Chem Soc. 2009 Jun 17; 131(23):8083-91. PMID: 19459633.
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    251. Baron R, Riley C, Chenprakhon P, Thotsaporn K, Winter RT, Alfieri A, Forneris F, van Berkel WJ, Chaiyen P, Fraaije MW, Mattevi A, McCammon JA. Multiple pathways guide oxygen diffusion into flavoenzyme active sites. Proc Natl Acad Sci U S A. 2009 Jun 30; 106(26):10603-8. PMID: 19541622.
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    252. Cheng X, Ivanov I, Wang H, Sine SM, McCammon JA. Molecular-dynamics simulations of ELIC-a prokaryotic homologue of the nicotinic acetylcholine receptor. Biophys J. 2009 Jun 03; 96(11):4502-13. PMID: 19486673.
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    253. Lu B, Cheng X, Huang J, McCammon JA. An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics. J Chem Theory Comput. 2009 Jun 09; 5(6):1692-1699. PMID: 19517026.
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    254. Wang HL, Toghraee R, Papke D, Cheng XL, McCammon JA, Ravaioli U, Sine SM. Single-channel current through nicotinic receptor produced by closure of binding site C-loop. Biophys J. 2009 May 06; 96(9):3582-90. PMID: 19413963.
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    255. McCammon JA. Darwinian biophysics: electrostatics and evolution in the kinetics of molecular binding. Proc Natl Acad Sci U S A. 2009 May 12; 106(19):7683-4. PMID: 19416830; PMCID: PMC2683110.
    256. Swift RV, McCammon JA. Substrate induced population shifts and stochastic gating in the PBCV-1 mRNA capping enzyme. J Am Chem Soc. 2009 Apr 15; 131(14):5126-33. PMID: 19301911.
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    257. Amaro RE, Cheng X, Ivanov I, Xu D, McCammon JA. Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations. J Am Chem Soc. 2009 Apr 08; 131(13):4702-9. PMID: 19296611.
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    258. Lawrenz M, Baron R, McCammon JA. Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. J Chem Theory Comput. 2009 Apr 14; 5(4):1106-1116. PMID: 19461872.
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    259. Ivetac A, McCammon JA. Elucidating the inhibition mechanism of HIV-1 non-nucleoside reverse transcriptase inhibitors through multicopy molecular dynamics simulations. J Mol Biol. 2009 May 08; 388(3):644-58. PMID: 19324058.
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    260. Grant BJ, Gorfe AA, McCammon JA. Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. PLoS Comput Biol. 2009 Mar; 5(3):e1000325. PMID: 19300489; PMCID: PMC2651530.
    261. Lu S, Michailova A, Saucerman J, Cheng Y, Yu Z, Kaiser T, Li W, Bank R, Holst M, McCammon J, Hayashi T, Hoshijima M, Arzberger P, McCulloch A. Multiscale modeling in rodent ventricular myocytes. IEEE Eng Med Biol Mag. 2009 Mar-Apr; 28(2):46-57. PMID: 19349251; PMCID: PMC3197248.
    262. Agrawal A, de Oliveira CA, Cheng Y, Jacobsen JA, McCammon JA, Cohen SM. Thioamide hydroxypyrothiones supersede amide hydroxypyrothiones in potency against anthrax lethal factor. J Med Chem. 2009 Feb 26; 52(4):1063-74. PMID: 19170530.
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    263. Khavrutskii IV, Gorfe AA, Lu B, McCammon JA. Free energy for the permeation of Na(+) and Cl(-) ions and their ion-pair through a zwitterionic dimyristoyl phosphatidylcholine lipid bilayer by umbrella integration with harmonic fourier beads. J Am Chem Soc. 2009 Feb 11; 131(5):1706-16. PMID: 19146415.
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    264. Cheng LT, Xie Y, Dzubiella J, McCammon JA, Che J, Li B. Coupling the Level-Set Method with Molecular Mechanics for Variational Implicit Solvation of Nonpolar Molecules. J Chem Theory Comput. 2009 Feb 10; 5(2):257-266. PMID: 20150952.
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    265. Xu D, Newhouse EI, Amaro RE, Pao HC, Cheng LS, Markwick PR, McCammon JA, Li WW, Arzberger PW. Distinct glycan topology for avian and human sialopentasaccharide receptor analogues upon binding different hemagglutinins: a molecular dynamics perspective. J Mol Biol. 2009 Mar 27; 387(2):465-91. PMID: 19356594.
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    266. Swift RV, Durrant J, Amaro RE, McCammon JA. Toward understanding the conformational dynamics of RNA ligation. Biochemistry. 2009 Feb 03; 48(4):709-19. PMID: 19133737; PMCID: PMC2651658.
    267. Durrant JD, Amaro RE, McCammon JA. AutoGrow: a novel algorithm for protein inhibitor design. Chem Biol Drug Des. 2009 Feb; 73(2):168-78. PMID: 19207419; PMCID: PMC2724963.
    268. Wong S, Amaro RE, McCammon JA. MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein Interface. J Chem Theory Comput. 2009 Feb 10; 5(2):422-429. PMID: 19461869.
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    269. Hamelberg D, McCammon JA. Mechanistic insight into the role of transition-state stabilization in cyclophilin A. J Am Chem Soc. 2009 Jan 14; 131(1):147-52. PMID: 19128175.
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    270. Babakhani A, Talley TT, Taylor P, McCammon JA. A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach. Comput Biol Chem. 2009 Apr; 33(2):160-70. PMID: 19186108.
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    271. Cheng Y, Holst MJ, McCammon JA. Finite element analysis of drug electrostatic diffusion: inhibition rate studies in N1 neuraminidase. Pac Symp Biocomput. 2009; 281-92. PMID: 19209708; PMCID: PMC3107071.
    272. Baron R, Wong SE, de Oliveira CA, McCammon JA. E9-Im9 colicin DNase-immunity protein biomolecular association in water: a multiple-copy and accelerated molecular dynamics simulation study. J Phys Chem B. 2008 Dec 25; 112(51):16802-14. PMID: 19053689.
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    273. Amaro RE, Schnaufer A, Interthal H, Hol W, Stuart KD, McCammon JA. Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei. Proc Natl Acad Sci U S A. 2008 Nov 11; 105(45):17278-83. PMID: 18981420.
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    274. Wong SE, Baron R, McCammon JA. Hot-spot residues at the E9/Im9 interface help binding via different mechanisms. Biopolymers. 2008 Nov; 89(11):916-20. PMID: 18546205.
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    275. Yu Z, Holst MJ, Hayashi T, Bajaj CL, Ellisman MH, McCammon JA, Hoshijima M. Three-dimensional geometric modeling of membrane-bound organelles in ventricular myocytes: bridging the gap between microscopic imaging and mathematical simulation. J Struct Biol. 2008 Dec; 164(3):304-13. PMID: 18835449; PMCID: PMC2790379.
    276. Khavrutskii IV, Fajer M, McCammon JA. Intrinsic Free Energy of the Conformational Transition of the KcsA Signature Peptide from Conducting to Nonconducting State. J Chem Theory Comput. 2008 Sep 09; 4(9):1541-1554. PMID: 20357907.
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    277. Fajer M, Hamelberg D, McCammon JA. Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration. J Chem Theory Comput. 2008 Oct 14; 4(10):1565-1569. PMID: 19461870.
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    278. Gorfe AA, McCammon JA. Similar membrane affinity of mono- and Di-S-acylated ras membrane anchors: a new twist in the role of protein lipidation. J Am Chem Soc. 2008 Sep 24; 130(38):12624-5. PMID: 18761454.
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    279. de Oliveira CA, Hamelberg D, McCammon JA. Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations. J Chem Theory Comput. 2008 Sep 09; 4(9):1516-1525. PMID: 19461868.
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    280. Cheng Y, Chang CE, Yu Z, Zhang Y, Sun M, Leyh TS, Holst MJ, McCammon JA. Diffusional channeling in the sulfate-activating complex: combined continuum modeling and coarse-grained brownian dynamics studies. Biophys J. 2008 Nov 15; 95(10):4659-67. PMID: 18689458; PMCID: PMC2576392.
    281. Babakhani A, Gorfe AA, Kim JE, McCammon JA. Thermodynamics of peptide insertion and aggregation in a lipid bilayer. J Phys Chem B. 2008 Aug 28; 112(34):10528-34. PMID: 18681475; PMCID: PMC2651738.
    282. Mura C, McCammon JA. Molecular dynamics of a kappaB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation. Nucleic Acids Res. 2008 Sep; 36(15):4941-55. PMID: 18653524.
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    283. Gorfe AA, Baron R, McCammon JA. Water-membrane partition thermodynamics of an amphiphilic lipopeptide: an enthalpy-driven hydrophobic effect. Biophys J. 2008 Oct; 95(7):3269-77. PMID: 18621822.
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    284. Cheng LS, Amaro RE, Xu D, Li WW, Arzberger PW, McCammon JA. Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem. 2008 Jul 10; 51(13):3878-94. PMID: 18558668; PMCID: PMC2652358.
    285. Gorfe AA, Grant BJ, McCammon JA. Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins. Structure. 2008 Jun; 16(6):885-96. PMID: 18547521; PMCID: PMC2519881.
    286. Chang CE, McLaughlin WA, Baron R, Wang W, McCammon JA. Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association. Proc Natl Acad Sci U S A. 2008 May 27; 105(21):7456-61. PMID: 18495919.
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    287. Baron R, McCammon JA. (Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding. Chemphyschem. 2008 May 16; 9(7):983-8. PMID: 18418822.
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    288. Cheng YH, Cheng XL, Radic Z, McCammon JA. Acetylcholinesterase: mechanisms of covalent inhibition of H447I mutant determined by computational analyses. Chem Biol Interact. 2008 Sep 25; 175(1-3):196-9. PMID: 18657802.
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    289. Gunatilleke SS, de Oliveira CA, McCammon JA, Barrios AM. Inhibition of cathepsin B by Au(I) complexes: a kinetic and computational study. J Biol Inorg Chem. 2008 May; 13(4):555-61. PMID: 18253767.
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    290. Zhou YC, Holst M, McCammon JA. A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces. J Math Anal Appl. 2008 Apr 01; 340(1):135-164. PMID: 19461946.
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    291. Swift RV, McCammon JA. Catalytically requisite conformational dynamics in the mRNA-capping enzyme probed by targeted molecular dynamics. Biochemistry. 2008 Apr 01; 47(13):4102-11. PMID: 18330997.
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    292. Che J, Dzubiella J, Li B, McCammon JA. Electrostatic free energy and its variations in implicit solvent models. J Phys Chem B. 2008 Mar 13; 112(10):3058-69. PMID: 18275182.
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    293. Abankwa D, Hanzal-Bayer M, Ariotti N, Plowman SJ, Gorfe AA, Parton RG, McCammon JA, Hancock JF. A novel switch region regulates H-ras membrane orientation and signal output. EMBO J. 2008 Mar 05; 27(5):727-35. PMID: 18273062.
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    294. Yu Z, Holst MJ, Cheng Y, McCammon JA. Feature-preserving adaptive mesh generation for molecular shape modeling and simulation. J Mol Graph Model. 2008 Jun; 26(8):1370-80. PMID: 18337134.
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    295. Wang HL, Cheng X, Taylor P, McCammon JA, Sine SM. Control of cation permeation through the nicotinic receptor channel. PLoS Comput Biol. 2008 Feb; 4(2):e41. PMID: 18282090.
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    296. Khavrutskii IV, Dzubiella J, McCammon JA. Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method. J Chem Phys. 2008 Jan 28; 128(4):044106. PMID: 18247929.
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    297. Lu B, McCammon JA. Molecular surface-free continuum model for electrodiffusion processes. Chem Phys Lett. 2008 Jan 21; 451(4-6):282-286. PMID: 19461944.
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    298. Landon MR, Amaro RE, Baron R, Ngan CH, Ozonoff D, McCammon JA, Vajda S. Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chem Biol Drug Des. 2008 Feb; 71(2):106-16. PMID: 18205727; PMCID: PMC2438278.
    299. Amaro RE, Baron R, McCammon JA. An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des. 2008 Sep; 22(9):693-705. PMID: 18196463.
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    300. Minh DD, McCammon JA. Springs and speeds in free energy reconstruction from irreversible single-molecule pulling experiments. J Phys Chem B. 2008 May 15; 112(19):5892-7. PMID: 18088108.
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    301. Zhou YC, Lu B, Huber GA, Holst MJ, McCammon JA. Continuum simulations of acetylcholine consumption by acetylcholinesterase: a Poisson-Nernst-Planck approach. J Phys Chem B. 2008 Jan 17; 112(2):270-5. PMID: 18052268.
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    302. Amaro RE, Swift RV, McCammon JA. Functional and structural insights revealed by molecular dynamics simulations of an essential RNA editing ligase in Trypanosoma brucei. PLoS Negl Trop Dis. 2007 Nov 14; 1(2):e68. PMID: 18060084; PMCID: PMC2100368.
    303. de Oliveira CA, Hamelberg D, McCammon JA. Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study. J Chem Phys. 2007 Nov 07; 127(17):175105. PMID: 17994855.
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    304. Hamelberg D, de Oliveira CA, McCammon JA. Sampling of slow diffusive conformational transitions with accelerated molecular dynamics. J Chem Phys. 2007 Oct 21; 127(15):155102. PMID: 17949218.
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    305. Minh DD, Hamelberg D, McCammon JA. Accelerated entropy estimates with accelerated dynamics. J Chem Phys. 2007 Oct 21; 127(15):154105. PMID: 17949130.
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    306. Cerutti DS, Baker NA, McCammon JA. Solvent reaction field potential inside an uncharged globular protein: a bridge between implicit and explicit solvent models? J Chem Phys. 2007 Oct 21; 127(15):155101. PMID: 17949217.
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    307. Lu B, Zhou YC, Huber GA, Bond SD, Holst MJ, McCammon JA. Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution. J Chem Phys. 2007 Oct 07; 127(13):135102. PMID: 17919055.
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    308. Gorfe AA, Chang CE, Ivanov I, McCammon JA. Dynamics of the acetylcholinesterase tetramer. Biophys J. 2008 Feb 15; 94(4):1144-54. PMID: 17921202.
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    309. Lu B, Cheng X, McCammon JA. "New-version-fast-multipole-method" accelerated electrostatic interactions in biomolecular systems. J Comput Phys. 2007 Oct 01; 226(2):1348-1366. PMID: 18379638.
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    310. Khavrutskii IV, McCammon JA. Generalized gradient-augmented harmonic Fourier beads method with multiple atomic and/or center-of-mass positional restraints. J Chem Phys. 2007 Sep 28; 127(12):124901. PMID: 17902931.
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    311. Gorfe AA, Babakhani A, McCammon JA. H-ras protein in a bilayer: interaction and structure perturbation. J Am Chem Soc. 2007 Oct 10; 129(40):12280-6. PMID: 17880077.
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    312. Hamelberg D, Shen T, McCammon JA. A proposed signaling motif for nuclear import in mRNA processing via the formation of arginine claw. Proc Natl Acad Sci U S A. 2007 Sep 18; 104(38):14947-51. PMID: 17823247.
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    313. Cheng LT, Dzubiella J, McCammon JA, Li B. Application of the level-set method to the implicit solvation of nonpolar molecules. J Chem Phys. 2007 Aug 28; 127(8):084503. PMID: 17764265.
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    314. Baron R, McCammon JA. Dynamics, hydration, and motional averaging of a loop-gated artificial protein cavity: the W191G mutant of cytochrome c peroxidase in water as revealed by molecular dynamics simulations. Biochemistry. 2007 Sep 18; 46(37):10629-42. PMID: 17718514.
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    315. Cheng X, Ivanov I, Wang H, Sine SM, McCammon JA. Nanosecond-timescale conformational dynamics of the human alpha7 nicotinic acetylcholine receptor. Biophys J. 2007 Oct 15; 93(8):2622-34. PMID: 17573436.
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    316. Ivanov I, Cheng X, Sine SM, McCammon JA. Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family. J Am Chem Soc. 2007 Jul 04; 129(26):8217-24. PMID: 17552523.
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    317. Amaro RE, Minh DD, Cheng LS, Lindstrom WM, Olson AJ, Lin JH, Li WW, McCammon JA. Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design. J Am Chem Soc. 2007 Jun 27; 129(25):7764-5. PMID: 17539643.
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    318. Lu B, McCammon JA. Improved Boundary Element Methods for Poisson-Boltzmann Electrostatic Potential and Force Calculations. J Chem Theory Comput. 2007 May; 3(3):1134-42. PMID: 26627432.
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    319. Sørensen J, Hamelberg D, Schiøtt B, McCammon JA. Comparative MD analysis of the stability of transthyretin providing insight into the fibrillation mechanism. Biopolymers. 2007 May; 86(1):73-82. PMID: 17315201.
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    320. Cheng Y, Cheng X, Radic Z, McCammon JA. Acetylcholinesterase: mechanisms of covalent inhibition of wild-type and H447I mutant determined by computational analyses. J Am Chem Soc. 2007 May 23; 129(20):6562-70. PMID: 17461584.
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    321. Grant BJ, McCammon JA, Caves LS, Cross RA. Multivariate analysis of conserved sequence-structure relationships in kinesins: coupling of the active site and a tubulin-binding sub-domain. J Mol Biol. 2007 May 18; 368(5):1231-48. PMID: 17399740.
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    322. Trylska J, Tozzini V, Chang CE, McCammon JA. HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics. Biophys J. 2007 Jun 15; 92(12):4179-87. PMID: 17384072.
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    323. Cheng Y, Suen JK, Zhang D, Bond SD, Zhang Y, Song Y, Baker NA, Bajaj CL, Holst MJ, McCammon JA. Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophys J. 2007 May 15; 92(10):3397-406. PMID: 17307827; PMCID: PMC1853150.
    324. Gorfe AA, Hanzal-Bayer M, Abankwa D, Hancock JF, McCammon JA. Structure and dynamics of the full-length lipid-modified H-Ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer. J Med Chem. 2007 Feb 22; 50(4):674-84. PMID: 17263520.
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    325. Ivanov I, Tainer JA, McCammon JA. Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV. Proc Natl Acad Sci U S A. 2007 Jan 30; 104(5):1465-70. PMID: 17242363.
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    326. Cheng Y, Suen JK, Radic Z, Bond SD, Holst MJ, McCammon JA. Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction models. Biophys Chem. 2007 May; 127(3):129-39. PMID: 17307283; PMCID: PMC2040065.
    327. Chang CE, Trylska J, Tozzini V, McCammon JA. Binding pathways of ligands to HIV-1 protease: coarse-grained and atomistic simulations. Chem Biol Drug Des. 2007 Jan; 69(1):5-13. PMID: 17313452.
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    328. Leduc PR, Wong MS, Ferreira PM, Groff RE, Haslinger K, Koonce MP, Lee WY, Love JC, McCammon JA, Monteiro-Riviere NA, Rotello VM, Rubloff GW, Westervelt R, Yoda M. Towards an in vivo biologically inspired nanofactory. Nat Nanotechnol. 2007 Jan; 2(1):3-7. PMID: 18654192.
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    329. Gorfe AA, Babakhani A, McCammon JA. Free energy profile of H-ras membrane anchor upon membrane insertion. Angew Chem Int Ed Engl. 2007; 46(43):8234-7. PMID: 17886310.
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    330. Ngo JC, Gullingsrud J, Giang K, Yeh MJ, Fu XD, Adams JA, McCammon JA, Ghosh G. SR protein kinase 1 is resilient to inactivation. Structure. 2007 Jan; 15(1):123-33. PMID: 17223538.
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    331. Mongan J, Simmerling C, McCammon JA, Case DA, Onufriev A. Generalized Born model with a simple, robust molecular volume correction. J Chem Theory Comput. 2007 Jan 01; 3(1):156-169. PMID: 21072141.
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    332. de Oliveira CA, Zissen M, Mongon J, McCammon JA. Molecular dynamics simulations of metalloproteinases types 2 and 3 reveal differences in the dynamic behavior of the S1' binding pocket. Curr Pharm Des. 2007; 13(34):3471-5. PMID: 18220784.
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    333. Swanson JM, Wagoner JA, Baker NA, McCammon JA. Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies:? Lessons Learned with Atom-Centered Dielectric Functions. J Chem Theory Comput. 2007 Jan; 3(1):170-83. PMID: 26627162.
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    334. Lu B, Cheng X, Huang J, McCammon JA. Order N algorithm for computation of electrostatic interactions in biomolecular systems. Proc Natl Acad Sci U S A. 2006 Dec 19; 103(51):19314-9. PMID: 17148613.
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    335. de Oliveira CA, Hamelberg D, McCammon JA. On the application of accelerated molecular dynamics to liquid water simulations. J Phys Chem B. 2006 Nov 16; 110(45):22695-701. PMID: 17092018.
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    336. Ivanov I, Chapados BR, McCammon JA, Tainer JA. Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications. Nucleic Acids Res. 2006; 34(20):6023-33. PMID: 17071716.
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    337. Senapati S, Cheng Y, McCammon JA. In-situ synthesis of a tacrine-triazole-based inhibitor of acetylcholinesterase: configurational selection imposed by steric interactions. J Med Chem. 2006 Oct 19; 49(21):6222-30. PMID: 17034128.
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    338. Bui JM, McCammon JA. Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanism. Proc Natl Acad Sci U S A. 2006 Oct 17; 103(42):15451-6. PMID: 17021015.
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    339. Yang G, Trylska J, Tor Y, McCammon JA. Binding of aminoglycosidic antibiotics to the oligonucleotide A-site model and 30S ribosomal subunit: Poisson-Boltzmann model, thermal denaturation, and fluorescence studies. J Med Chem. 2006 Sep 07; 49(18):5478-90. PMID: 16942021.
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    340. Hamelberg D, Shen T, McCammon JA. Insight into the role of hydration on protein dynamics. J Chem Phys. 2006 Sep 07; 125(9):094905. PMID: 16965117.
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    341. Jain T, Cerutti DS, McCammon JA. Configurational-bias sampling technique for predicting side-chain conformations in proteins. Protein Sci. 2006 Sep; 15(9):2029-39. PMID: 16943441.
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    342. Grant BJ, Rodrigues AP, ElSawy KM, McCammon JA, Caves LS. Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics. 2006 Nov 01; 22(21):2695-6. PMID: 16940322.
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    343. Tozzini V, Trylska J, Chang CE, McCammon JA. Flap opening dynamics in HIV-1 protease explored with a coarse-grained model. J Struct Biol. 2007 Mar; 157(3):606-15. PMID: 17029846.
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    344. Cheng X, Wang H, Grant B, Sine SM, McCammon JA. Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors. PLoS Comput Biol. 2006 Sep 29; 2(9):e134. PMID: 17009865; PMCID: PMC1584325.
    345. Cerutti DS, Jain T, McCammon JA. CIRSE: a solvation energy estimator compatible with flexible protein docking and design applications. Protein Sci. 2006 Jul; 15(7):1579-96. PMID: 16815913.
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    346. Lewis JA, Mongan J, McCammon JA, Cohen SM. Evaluation and binding-mode prediction of thiopyrone-based inhibitors of anthrax lethal factor. ChemMedChem. 2006 Jul; 1(7):694-7. PMID: 16902919.
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    347. Perryman AL, Lin JH, McCammon JA. Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug design. Biopolymers. 2006 Jun 15; 82(3):272-84. PMID: 16508951.
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    348. Konecny R, Trylska J, Tama F, Zhang D, Baker NA, Brooks CL, McCammon JA. Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers. 2006 Jun 05; 82(2):106-20. PMID: 16278831.
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    349. Minh DD, Chang CE, Trylska J, Tozzini V, McCammon JA. The influence of macromolecular crowding on HIV-1 protease internal dynamics. J Am Chem Soc. 2006 May 10; 128(18):6006-7. PMID: 16669648.
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    350. Adcock SA, McCammon JA. Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev. 2006 May; 106(5):1589-615. PMID: 16683746.
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    351. Hamacher K, McCammon JA. Computing the Amino Acid Specificity of Fluctuations in Biomolecular Systems. J Chem Theory Comput. 2006 May; 2(3):873-8. PMID: 26626694.
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    352. Hamacher K, Hübsch A, McCammon JA. A minimal model for stabilization of biomolecules by hydrocarbon cross-linking. J Chem Phys. 2006 Apr 28; 124(16):164907. PMID: 16674170.
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    353. Ung MU, Lu B, McCammon JA. E230Q mutation of the catalytic subunit of cAMP-dependent protein kinase affects local structure and the binding of peptide inhibitor. Biopolymers. 2006 Apr 15; 81(6):428-39. PMID: 16365849.
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    354. Shen T, Hamelberg D, McCammon JA. Elasticity of peptide omega bonds. Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Apr; 73(4 Pt 1):041908. PMID: 16711837.
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    355. Chang CE, Shen T, Trylska J, Tozzini V, McCammon JA. Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model. Biophys J. 2006 Jun 01; 90(11):3880-5. PMID: 16533835.
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    356. Zhang D, Gullingsrud J, McCammon JA. Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain. J Am Chem Soc. 2006 Mar 08; 128(9):3019-26. PMID: 16506783.
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    357. Cheng Y, Zhang Y, McCammon JA. How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: a theoretical study. Protein Sci. 2006 Apr; 15(4):672-83. PMID: 16522793.
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    358. Dzubiella J, Swanson JM, McCammon JA. Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models. Phys Rev Lett. 2006 Mar 03; 96(8):087802. PMID: 16606226.
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    359. Dzubiella J, Swanson JM, McCammon JA. Coupling nonpolar and polar solvation free energies in implicit solvent models. J Chem Phys. 2006 Feb 28; 124(8):084905. PMID: 16512740.
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    360. Hamacher K, Trylska J, McCammon JA. Dependency map of proteins in the small ribosomal subunit. PLoS Comput Biol. 2006 Feb; 2(2):e10. PMID: 16485038.
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    361. Ivanov I, Vemparala S, Pophristic V, Kuroda K, DeGrado WF, McCammon JA, Klein ML. Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamics. J Am Chem Soc. 2006 Feb 15; 128(6):1778-9. PMID: 16464062.
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    362. Bui JM, Radic Z, Taylor P, McCammon JA. Conformational transitions in protein-protein association: binding of fasciculin-2 to acetylcholinesterase. Biophys J. 2006 May 01; 90(9):3280-7. PMID: 16473897; PMCID: PMC1432132.
    363. Tozzini V, Rocchia W, McCammon JA. Mapping all-atom models onto one-bead Coarse Grained Models: general properties and applications to a minimal polypeptide model. J Chem Theory Comput. 2006; 2(3):667-673. PMID: 19461947.
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    364. Gullingsrud J, Kim C, Taylor SS, McCammon JA. Dynamic binding of PKA regulatory subunit RI alpha. Structure. 2006 Jan; 14(1):141-9. PMID: 16407073.
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    365. Senapati S, Bui JM, McCammon JA. Induced fit in mouse acetylcholinesterase upon binding a femtomolar inhibitor: a molecular dynamics study. J Med Chem. 2005 Dec 29; 48(26):8155-62. PMID: 16366597.
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    366. Bui JM, McCammon JA. Acetylcholinesterase: pivotal roles of its long omega loop (Cys69-Cys96) in regulating substrate binding. Chem Biol Interact. 2005 Dec 15; 157-158:357-9. PMID: 16429484.
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    367. Vigil D, Lin JH, Sotriffer CA, Pennypacker JK, McCammon JA, Taylor SS. A simple electrostatic switch important in the activation of type I protein kinase A by cyclic AMP. Protein Sci. 2006 Jan; 15(1):113-21. PMID: 16322564; PMCID: PMC2242374.
    368. Wong CF, Kua J, Zhang Y, Straatsma TP, McCammon JA. Molecular docking of balanol to dynamics snapshots of protein kinase A. Proteins. 2005 Dec 01; 61(4):850-8. PMID: 16245317.
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    369. Zhang D, McCammon JA. The association of tetrameric acetylcholinesterase with ColQ tail: a block normal mode analysis. PLoS Comput Biol. 2005 Nov; 1(6):e62. PMID: 16299589.
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    370. Giorgione JR, Lin JH, McCammon JA, Newton AC. Increased membrane affinity of the C1 domain of protein kinase Cdelta compensates for the lack of involvement of its C2 domain in membrane recruitment. J Biol Chem. 2006 Jan 20; 281(3):1660-9. PMID: 16293612; PMCID: PMC2913972.
    371. Cheng X, Lu B, Grant B, Law RJ, McCammon JA. Channel opening motion of alpha7 nicotinic acetylcholine receptor as suggested by normal mode analysis. J Mol Biol. 2006 Jan 13; 355(2):310-24. PMID: 16307758.
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    372. Puerta DT, Mongan J, Tran BL, McCammon JA, Cohen SM. Potent, selective pyrone-based inhibitors of stromelysin-1. J Am Chem Soc. 2005 Oct 19; 127(41):14148-9. PMID: 16218585.
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    373. Hamelberg D, McCammon JA. Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease. J Am Chem Soc. 2005 Oct 12; 127(40):13778-9. PMID: 16201784.
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    374. McCammon JA. Target flexibility in molecular recognition. Biochim Biophys Acta. 2005 Dec 30; 1754(1-2):221-4. PMID: 16181817.
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    375. Shen T, Zong C, Hamelberg D, McCammon JA, Wolynes PG. The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain. FASEB J. 2005 Sep; 19(11):1389-95. PMID: 16126906.
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    376. Lu B, Cheng X, Hou T, McCammon JA. Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals. J Chem Phys. 2005 Aug 22; 123(8):084904. PMID: 16164327.
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    377. Minh DD, Bui JM, Chang CE, Jain T, Swanson JM, McCammon JA. The entropic cost of protein-protein association: a case study on acetylcholinesterase binding to fasciculin-2. Biophys J. 2005 Oct; 89(4):L25-7. PMID: 16100267.
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    378. Swanson JM, Mongan J, McCammon JA. Limitations of atom-centered dielectric functions in implicit solvent models. J Phys Chem B. 2005 Aug 11; 109(31):14769-72. PMID: 16852866.
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    379. Trylska J, McCammon JA, Brooks Iii CL. Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach. J Am Chem Soc. 2005 Aug 10; 127(31):11125-33. PMID: 16076220.
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    380. Trylska J, Tozzini V, McCammon JA. Exploring global motions and correlations in the ribosome. Biophys J. 2005 Sep; 89(3):1455-63. PMID: 15951386.
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    381. Lu B, Zhang D, McCammon JA. Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method. J Chem Phys. 2005 Jun 01; 122(21):214102. PMID: 15974723.
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    382. Dzubiella J, McCammon JA. Substrate concentration dependence of the diffusion-controlled steady-state rate constant. J Chem Phys. 2005 May 08; 122(18):184902. PMID: 15918760.
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    383. Sims PA, Wong CF, Vuga D, McCammon JA, Sefton BM. Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems. J Comput Chem. 2005 May; 26(7):668-81. PMID: 15754303.
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    384. Swanson JM, Adcock SA, McCammon JA. Optimized Radii for Poisson-Boltzmann Calculations with the AMBER Force Field. J Chem Theory Comput. 2005 May; 1(3):484-93. PMID: 26641515.
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    385. Law RJ, Henchman RH, McCammon JA. A gating mechanism proposed from a simulation of a human alpha7 nicotinic acetylcholine receptor. Proc Natl Acad Sci U S A. 2005 May 10; 102(19):6813-8. PMID: 15857954.
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    386. Hamelberg D, Shen T, McCammon JA. Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis. J Am Chem Soc. 2005 Feb 16; 127(6):1969-74. PMID: 15701032.
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    387. Cheng Y, Zhang Y, McCammon JA. How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study. J Am Chem Soc. 2005 Feb 09; 127(5):1553-62. PMID: 15686389.
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    388. Henchman RH, Wang HL, Sine SM, Taylor P, McCammon JA. Ligand-induced conformational change in the alpha7 nicotinic receptor ligand binding domain. Biophys J. 2005 Apr; 88(4):2564-76. PMID: 15665135.
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    389. Lu B, Wong CF, McCammon JA. Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation study. Protein Sci. 2005 Jan; 14(1):159-68. PMID: 15608120.
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    390. Cerutti DS, Ten Eyck LF, McCammon JA. Rapid Estimation of Solvation Energy for Simulations of Protein-Protein Association. J Chem Theory Comput. 2005 Jan; 1(1):143-52. PMID: 26641125.
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    391. Zhang D, Suen J, Zhang Y, Song Y, Radic Z, Taylor P, Holst MJ, Bajaj C, Baker NA, McCammon JA. Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophys J. 2005 Mar; 88(3):1659-65. PMID: 15626705; PMCID: PMC1305222.
    392. Gao F, Bren N, Burghardt TP, Hansen S, Henchman RH, Taylor P, McCammon JA, Sine SM. Agonist-mediated conformational changes in acetylcholine-binding protein revealed by simulation and intrinsic tryptophan fluorescence. J Biol Chem. 2005 Mar 04; 280(9):8443-51. PMID: 15591050.
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    393. Mongan J, Case DA, McCammon JA. Constant pH molecular dynamics in generalized Born implicit solvent. J Comput Chem. 2004 Dec; 25(16):2038-48. PMID: 15481090.
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    394. Zhang D, Konecny R, Baker NA, McCammon JA. Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach. Biopolymers. 2004 Nov; 75(4):325-37. PMID: 15386271.
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    395. Senapati S, Wong CF, McCammon JA. Finite concentration effects on diffusion-controlled reactions. J Chem Phys. 2004 Oct 22; 121(16):7896-900. PMID: 15485251.
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    396. Trylska J, Konecny R, Tama F, Brooks CL, McCammon JA. Ribosome motions modulate electrostatic properties. Biopolymers. 2004 Aug 15; 74(6):423-31. PMID: 15274086.
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    397. Sims PA, Wong CF, McCammon JA. Charge optimization of the interface between protein kinases and their ligands. J Comput Chem. 2004 Aug; 25(11):1416-29. PMID: 15185335.
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    398. Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 2004 Jul 01; 32(Web Server issue):W665-7. PMID: 15215472.
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    399. Hamelberg D, McCammon JA. Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method. J Am Chem Soc. 2004 Jun 23; 126(24):7683-9. PMID: 15198616.
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    400. Hamelberg D, Mongan J, McCammon JA. Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J Chem Phys. 2004 Jun 22; 120(24):11919-29. PMID: 15268227.
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    401. Bui JM, Tai K, McCammon JA. Acetylcholinesterase: enhanced fluctuations and alternative routes to the active site in the complex with fasciculin-2. J Am Chem Soc. 2004 Jun 16; 126(23):7198-205. PMID: 15186156.
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    402. Schames JR, Henchman RH, Siegel JS, Sotriffer CA, Ni H, McCammon JA. Discovery of a novel binding trench in HIV integrase. J Med Chem. 2004 Apr 08; 47(8):1879-81. PMID: 15055986.
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    403. Perryman AL, Lin JH, McCammon JA. HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs. Protein Sci. 2004 Apr; 13(4):1108-23. PMID: 15044738.
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    404. Song Y, Zhang Y, Shen T, Bajaj CL, McCammon JA, Baker NA. Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophys J. 2004 Apr; 86(4):2017-29. PMID: 15041644.
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    405. Trylska J, Grochowski P, McCammon JA. The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease. Protein Sci. 2004 Feb; 13(2):513-28. PMID: 14739332.
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    406. Swanson JM, Henchman RH, McCammon JA. Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys J. 2004 Jan; 86(1 Pt 1):67-74. PMID: 14695250.
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    407. Kua J, Zhang Y, Eslami AC, Butler JR, McCammon JA. Studying the roles of W86, E202, and Y337 in binding of acetylcholine to acetylcholinesterase using a combined molecular dynamics and multiple docking approach. Protein Sci. 2003 Dec; 12(12):2675-84. PMID: 14627729.
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    408. Henchman RH, Wang HL, Sine SM, Taylor P, McCammon JA. Asymmetric structural motions of the homomeric alpha7 nicotinic receptor ligand binding domain revealed by molecular dynamics simulation. Biophys J. 2003 Nov; 85(5):3007-18. PMID: 14581202.
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    409. Cerutti DS, Wong CF, McCammon JA. Brownian dynamics simulations of ion atmospheres around polyalanine and B-DNA: effects of biomolecular dielectric. Biopolymers. 2003 Oct; 70(3):391-402. PMID: 14579311.
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    410. Shen T, Wong CF, McCammon JA. Brownian dynamics simulation of helix-capping motifs. Biopolymers. 2003 Oct; 70(2):252-9. PMID: 14517913.
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    411. Sept D, Baker NA, McCammon JA. The physical basis of microtubule structure and stability. Protein Sci. 2003 Oct; 12(10):2257-61. PMID: 14500883.
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    412. Bui JM, Henchman RH, McCammon JA. The dynamics of ligand barrier crossing inside the acetylcholinesterase gorge. Biophys J. 2003 Oct; 85(4):2267-72. PMID: 14507691.
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    413. Morikis D, Elcock AH, Jennings PA, McCammon JA. The pH dependence of stability of the activation helix and the catalytic site of GART. Biophys Chem. 2003 Sep; 105(2-3):279-91. PMID: 14499900.
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    414. Nielsen JE, McCammon JA. Calculating pKa values in enzyme active sites. Protein Sci. 2003 Sep; 12(9):1894-901. PMID: 12930989.
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    415. Puerta DT, Schames JR, Henchman RH, McCammon JA, Cohen SM. From model complexes to metalloprotein inhibition: a synergistic approach to structure-based drug discovery. Angew Chem Int Ed Engl. 2003 Aug 18; 42(32):3772-4. PMID: 12923840.
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    416. Sims PA, Wong CF, McCammon JA. A computational model of binding thermodynamics: the design of cyclin-dependent kinase 2 inhibitors. J Med Chem. 2003 Jul 17; 46(15):3314-25. PMID: 12852762.
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    417. Shi J, Tai K, McCammon JA, Taylor P, Johnson DA. Nanosecond dynamics of the mouse acetylcholinesterase cys69-cys96 omega loop. J Biol Chem. 2003 Aug 15; 278(33):30905-11. PMID: 12759360.
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    418. Tai K, Bond SD, MacMillan HR, Baker NA, Holst MJ, McCammon JA. Finite element simulations of acetylcholine diffusion in neuromuscular junctions. Biophys J. 2003 Apr; 84(4):2234-41. PMID: 12668432; PMCID: PMC1302790.
    419. Nielsen JE, McCammon JA. On the evaluation and optimization of protein X-ray structures for pKa calculations. Protein Sci. 2003 Feb; 12(2):313-26. PMID: 12538895.
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    420. Lin JH, Perryman AL, Schames JR, McCammon JA. The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers. 2003 Jan; 68(1):47-62. PMID: 12579579.
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    421. Baker NA, McCammon JA. Electrostatic interactions. Methods Biochem Anal. 2003; 44:427-40. PMID: 12647398.
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    422. Podtelezhnikov AA, Gao K, Bushman FD, McCammon JA. Modeling HIV-1 integrase complexes based on their hydrodynamic properties. Biopolymers. 2003 Jan; 68(1):110-20. PMID: 12579583.
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    423. Perryman AL, McCammon JA. AutoDocking dinucleotides to the HIV-1 integrase core domain: exploring possible binding sites for viral and genomic DNA. J Med Chem. 2002 Dec 19; 45(26):5624-7. PMID: 12477345.
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    424. Rowley DC, Hansen MS, Rhodes D, Sotriffer CA, Ni H, McCammon JA, Bushman FD, Fenical W. Thalassiolins A-C: new marine-derived inhibitors of HIV cDNA integrase. Bioorg Med Chem. 2002 Nov; 10(11):3619-25. PMID: 12213478.
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    425. Zhang Y, Kua J, McCammon JA. Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study. J Am Chem Soc. 2002 Sep 04; 124(35):10572-7. PMID: 12197759.
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    426. Lin JH, Baker NA, McCammon JA. Bridging implicit and explicit solvent approaches for membrane electrostatics. Biophys J. 2002 Sep; 83(3):1374-9. PMID: 12202363.
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    427. Henchman RH, McCammon JA. Structural and dynamic properties of water around acetylcholinesterase. Protein Sci. 2002 Sep; 11(9):2080-90. PMID: 12192064.
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    428. Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nat Struct Biol. 2002 Sep; 9(9):646-52. PMID: 12198485.
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    429. Shen T, Canino LS, McCammon JA. Unfolding proteins under external forces: a solvable model under the self-consistent pair contact probability approximation. Phys Rev Lett. 2002 Aug 05; 89(6):068103. PMID: 12190614.
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    430. Kua J, Zhang Y, McCammon JA. Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach. J Am Chem Soc. 2002 Jul 17; 124(28):8260-7. PMID: 12105904.
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    431. Henchman RH, McCammon JA. Extracting hydration sites around proteins from explicit water simulations. J Comput Chem. 2002 Jul 15; 23(9):861-9. PMID: 11984847.
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    432. Shen T, Tai K, Henchman RH, McCammon JA. Molecular dynamics of acetylcholinesterase. Acc Chem Res. 2002 Jun; 35(6):332-40. PMID: 12069617.
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    433. Tai K, Shen T, Henchman RH, Bourne Y, Marchot P, McCammon JA. Mechanism of acetylcholinesterase inhibition by fasciculin: a 5-ns molecular dynamics simulation. J Am Chem Soc. 2002 May 29; 124(21):6153-61. PMID: 12022850.
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    434. Lin JH, Perryman AL, Schames JR, McCammon JA. Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J Am Chem Soc. 2002 May 22; 124(20):5632-3. PMID: 12010024.
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    435. Henchman RH, Tai K, Shen T, McCammon JA. Properties of water molecules in the active site gorge of acetylcholinesterase from computer simulation. Biophys J. 2002 May; 82(5):2671-82. PMID: 11964254.
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    436. Ma C, Baker NA, Joseph S, McCammon JA. Binding of aminoglycoside antibiotics to the small ribosomal subunit: a continuum electrostatics investigation. J Am Chem Soc. 2002 Feb 20; 124(7):1438-42. PMID: 11841313.
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    437. Wong CF, McCammon JA. Protein flexibility and computer-aided drug design. Annu Rev Pharmacol Toxicol. 2003; 43:31-45. PMID: 12142469.
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    438. Morikis D, Elcock AH, Jennings PA, McCammon JA. Native-state conformational dynamics of GART: a regulatory pH-dependent coil-helix transition examined by electrostatic calculations. Protein Sci. 2001 Nov; 10(11):2363-78. PMID: 11604542.
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    439. Morikis D, Elcock AH, Jennings PA, McCammon JA. Proton transfer dynamics of GART: the pH-dependent catalytic mechanism examined by electrostatic calculations. Protein Sci. 2001 Nov; 10(11):2379-92. PMID: 11604543.
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    440. Andrianantoandro E, Blanchoin L, Sept D, McCammon JA, Pollard TD. Kinetic mechanism of end-to-end annealing of actin filaments. J Mol Biol. 2001 Sep 28; 312(4):721-30. PMID: 11575927.
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    441. Shen T, Wong CF, McCammon JA. Atomistic Brownian dynamics simulation of peptide phosphorylation. J Am Chem Soc. 2001 Sep 19; 123(37):9107-11. PMID: 11552818.
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    442. Ni H, Sotriffer CA, McCammon JA. Ordered water and ligand mobility in the HIV-1 integrase-5CITEP complex: a molecular dynamics study. J Med Chem. 2001 Sep 13; 44(19):3043-7. PMID: 11543671.
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    443. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A. 2001 Aug 28; 98(18):10037-41. PMID: 11517324.
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    444. Tai K, Shen T, Börjesson U, Philippopoulos M, McCammon JA. Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase. Biophys J. 2001 Aug; 81(2):715-24. PMID: 11463620.
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    445. Sept D, McCammon JA. Thermodynamics and kinetics of actin filament nucleation. Biophys J. 2001 Aug; 81(2):667-74. PMID: 11463615.
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    446. Wong CF, Hünenberger PH, Akamine P, Narayana N, Diller T, McCammon JA, Taylor S, Xuong NH. Computational analysis of PKA-balanol interactions. J Med Chem. 2001 May 10; 44(10):1530-9. PMID: 11334563.
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    447. Ondrechen MJ, Briggs JM, McCammon JA. A model for enzyme-substrate interaction in alanine racemase. J Am Chem Soc. 2001 Mar 28; 123(12):2830-4. PMID: 11456969.
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    448. Shen TY, Tai K, McCammon JA. Statistical analysis of the fractal gating motions of the enzyme acetylcholinesterase. Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Apr; 63(4 Pt 1):041902. PMID: 11308872.
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    449. Elcock AH, McCammon JA. Calculation of weak protein-protein interactions: the pH dependence of the second virial coefficient. Biophys J. 2001 Feb; 80(2):613-25. PMID: 11159430.
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    450. Nolen B, Yun CY, Wong CF, McCammon JA, Fu XD, Ghosh G. The structure of Sky1p reveals a novel mechanism for constitutive activity. Nat Struct Biol. 2001 Feb; 8(2):176-83. PMID: 11175909.
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    451. Sotriffer CA, Ni H, McCammon JA. Active site binding modes of HIV-1 integrase inhibitors. J Med Chem. 2000 Nov 02; 43(22):4109-17. PMID: 11063607.
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    452. Bala P, Grochowski P, Nowinski K, Lesyng B, McCammon JA. Quantum-dynamical picture of a multistep enzymatic process: reaction catalyzed by phospholipase A(2). Biophys J. 2000 Sep; 79(3):1253-62. PMID: 10968989.
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    453. Carlson HA, Masukawa KM, Rubins K, Bushman FD, Jorgensen WL, Lins RD, Briggs JM, McCammon JA. Developing a dynamic pharmacophore model for HIV-1 integrase. J Med Chem. 2000 Jun 01; 43(11):2100-14. PMID: 10841789.
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    454. Brown FL, Leitner DM, McCammon JA, Wilson KR. Lateral diffusion of membrane proteins in the presence of static and dynamic corrals: suggestions for appropriate observables. Biophys J. 2000 May; 78(5):2257-69. PMID: 10777724.
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    455. Wlodek ST, Shen T, McCammon JA. Electrostatic steering of substrate to acetylcholinesterase: analysis of field fluctuations. Biopolymers. 2000 Mar; 53(3):265-71. PMID: 10679631.
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    456. Carlson HA, McCammon JA. Accommodating protein flexibility in computational drug design. Mol Pharmacol. 2000 Feb; 57(2):213-8. PMID: 10648630.
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    457. Sept D, Elcock AH, McCammon JA. Computer simulations of actin polymerization can explain the barbed-pointed end asymmetry. J Mol Biol. 1999 Dec 17; 294(5):1181-9. PMID: 10600376.
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    458. Sept D, Xu J, Pollard TD, McCammon JA. Annealing accounts for the length of actin filaments formed by spontaneous polymerization. Biophys J. 1999 Dec; 77(6):2911-9. PMID: 10585915.
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    459. Tara S, Helms V, Straatsma TP, McCammon JA. Molecular dynamics of mouse acetylcholinesterase complexed with huperzine A. Biopolymers. 1999 Oct 05; 50(4):347-59. PMID: 10423544.
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    460. Baker NA, Helms V, McCammon JA. Dynamical properties of fasciculin-2. Proteins. 1999 Sep 01; 36(4):447-53. PMID: 10450086.
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    461. Elcock AH, Gabdoulline RR, Wade RC, McCammon JA. Computer simulation of protein-protein association kinetics: acetylcholinesterase-fasciculin. J Mol Biol. 1999 Aug 06; 291(1):149-62. PMID: 10438612.
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    462. Tara S, Straatsma TP, McCammon JA. Mouse acetylcholinesterase unliganded and in complex with huperzine A: a comparison of molecular dynamics simulations. Biopolymers. 1999 Jul; 50(1):35-43. PMID: 10341665.
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    463. Lins RD, Briggs JM, Straatsma TP, Carlson HA, Greenwald J, Choe S, McCammon JA. Molecular dynamics studies on the HIV-1 integrase catalytic domain. Biophys J. 1999 Jun; 76(6):2999-3011. PMID: 10354426.
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    464. Weber W, Helms V, McCammon JA, Langhoff PW. Shedding light on the dark and weakly fluorescent states of green fluorescent proteins. Proc Natl Acad Sci U S A. 1999 May 25; 96(11):6177-82. PMID: 10339561.
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    465. Hünenberger PH, McCammon JA. Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study. Biophys Chem. 1999 Apr 05; 78(1-2):69-88. PMID: 10343384.
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    466. Wriggers W, Milligan RA, McCammon JA. Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. J Struct Biol. 1999 Apr-May; 125(2-3):185-95. PMID: 10222274.
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    467. Smart JL, McCammon JA. Phosphorylation stabilizes the N-termini of alpha-helices. Biopolymers. 1999 Mar; 49(3):225-33. PMID: 9990840.
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    468. Hünenberger PH, Helms V, Narayana N, Taylor SS, McCammon JA. Determinants of ligand binding to cAMP-dependent protein kinase. Biochemistry. 1999 Feb 23; 38(8):2358-66. PMID: 10029529.
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    469. de Bakker PI, Hünenberger PH, McCammon JA. Molecular dynamics simulations of the hyperthermophilic protein sac7d from Sulfolobus acidocaldarius: contribution of salt bridges to thermostability. J Mol Biol. 1999 Jan 29; 285(4):1811-30. PMID: 9917414.
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    470. Carlson HA, Briggs JM, McCammon JA. Calculation of the pKa values for the ligands and side chains of Escherichia coli D-alanine:D-alanine ligase. J Med Chem. 1999 Jan 14; 42(1):109-17. PMID: 9888837.
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    471. Blachut-Okrasinska E, Lesyng B, Briggs JM, McCammon JA, Antosiewicz JM. Poisson-Boltzmann model studies of molecular electrostatic properties of the cAMP-dependent protein kinase. Eur Biophys J. 1999; 28(6):457-67. PMID: 10460339.
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    472. Wriggers W, Milligan RA, Schulten K, McCammon JA. Self-organizing neural networks bridge the biomolecular resolution gap. J Mol Biol. 1998 Dec 18; 284(5):1247-54. PMID: 9878345.
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    473. Tara S, Elcock AH, Kirchhoff PD, Briggs JM, Radic Z, Taylor P, McCammon JA. Rapid binding of a cationic active site inhibitor to wild type and mutant mouse acetylcholinesterase: Brownian dynamics simulation including diffusion in the active site gorge. Biopolymers. 1998 Dec; 46(7):465-74. PMID: 9838872.
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    474. Weber W, Demirdjian H, Lins RD, Briggs JM, Ferreira R, McCammon JA. Brownian and essential dynamics studies of the HIV-1 integrase catalytic domain. J Biomol Struct Dyn. 1998 Dec; 16(3):733-45. PMID: 10052629.
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    475. Smart JL, McCammon JA. Analysis of synaptic transmission in the neuromuscular junction using a continuum finite element model. Biophys J. 1998 Oct; 75(4):1679-88. PMID: 9746510.
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    476. Elcock AH, McCammon JA. Electrostatic contributions to the stability of halophilic proteins. J Mol Biol. 1998 Jul 24; 280(4):731-48. PMID: 9677300.
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    477. McCammon JA. Theory of biomolecular recognition. Curr Opin Struct Biol. 1998 Apr; 8(2):245-9. PMID: 9631300.
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    478. Zhou HX, Briggs JM, Tara S, McCammon JA. Correlation between rate of enzyme-substrate diffusional encounter and average Boltzmann factor around active site. Biopolymers. 1998 Apr; 45(5):355-60. PMID: 9530014.
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    479. Marrone TJ, Resat H, Hodge CN, Chang CH, McCammon JA. Solvation studies of DMP323 and A76928 bound to HIV protease: analysis of water sites using grand canonical Monte Carlo simulations. Protein Sci. 1998 Mar; 7(3):573-9. PMID: 9541388.
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    480. Elcock AH, Huber GA, McCammon JA. Electrostatic channeling of substrates between enzyme active sites: comparison of simulation and experiment. Biochemistry. 1997 Dec 23; 36(51):16049-58. PMID: 9405038.
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    481. Gibas CJ, Subramaniam S, McCammon JA, Braden BC, Poljak RJ. pH dependence of antibody/lysozyme complexation. Biochemistry. 1997 Dec 16; 36(50):15599-614. PMID: 9398288.
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    482. Helms V, McCammon JA. Kinase conformations: a computational study of the effect of ligand binding. Protein Sci. 1997 Nov; 6(11):2336-43. PMID: 9385635.
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    483. Baginski M, Resat H, McCammon JA. Molecular properties of amphotericin B membrane channel: a molecular dynamics simulation. Mol Pharmacol. 1997 Oct; 52(4):560-70. PMID: 9380018.
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    484. Radic Z, Kirchhoff PD, Quinn DM, McCammon JA, Taylor P. Electrostatic influence on the kinetics of ligand binding to acetylcholinesterase. Distinctions between active center ligands and fasciculin. J Biol Chem. 1997 Sep 12; 272(37):23265-77. PMID: 9287336.
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    485. Taylor P, Ross EM, Sternweis PC, Neubig RR, McCammon JA. Colloquium on signaling and molecular structure in pharmacology (La Jolla, California, March 11-12, 1997). Mol Pharmacol. 1997 Jul; 52(1):1-5. PMID: 9224805.
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    486. Allison SA, Potter M, McCammon JA. Modeling the electrophoresis of lysozyme. II. Inclusion of ion relaxation. Biophys J. 1997 Jul; 73(1):133-40. PMID: 9199778.
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    487. Antosiewicz J, Miller MD, Krause KL, McCammon JA. Simulation of electrostatic and hydrodynamic properties of Serratia endonuclease. Biopolymers. 1997 Apr 05; 41(4):443-50. PMID: 9080779.
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    488. Fogolari F, Elcock AH, Esposito G, Viglino P, Briggs JM, McCammon JA. Electrostatic effects in homeodomain-DNA interactions. J Mol Biol. 1997 Mar 28; 267(2):368-81. PMID: 9096232.
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    489. Gilson MK, Given JA, Bush BL, McCammon JA. The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys J. 1997 Mar; 72(3):1047-69. PMID: 9138555.
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    490. Wlodek ST, Antosiewicz J, McCammon JA. Prediction of titration properties of structures of a protein derived from molecular dynamics trajectories. Protein Sci. 1997 Feb; 6(2):373-82. PMID: 9041639.
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    491. Resat H, Marrone TJ, McCammon JA. Enzyme-inhibitor association thermodynamics: explicit and continuum solvent studies. Biophys J. 1997 Feb; 72(2 Pt 1):522-32. PMID: 9017183.
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    492. Marrone TJ, Briggs JM, McCammon JA. Structure-based drug design: computational advances. Annu Rev Pharmacol Toxicol. 1997; 37:71-90. PMID: 9131247.
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    493. McCammon JA. A speed limit for protein folding. Proc Natl Acad Sci U S A. 1996 Oct 15; 93(21):11426-7. PMID: 8876151.
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    494. Elcock AH, McCammon JA. Evidence for electrostatic channeling in a fusion protein of malate dehydrogenase and citrate synthase. Biochemistry. 1996 Oct 01; 35(39):12652-8. PMID: 8841108.
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    495. Elcock AH, Potter MJ, Matthews DA, Knighton DR, McCammon JA. Electrostatic channeling in the bifunctional enzyme dihydrofolate reductase-thymidylate synthase. J Mol Biol. 1996 Sep 27; 262(3):370-4. PMID: 8845002.
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    496. Antosiewicz J, Wlodek ST, McCammon JA. Acetylcholinesterase: role of the enzyme's charge distribution in steering charged ligands toward the active site. Biopolymers. 1996 Jul; 39(1):85-94. PMID: 8924629.
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    497. Antosiewicz J, McCammon JA, Gilson MK. The determinants of pKas in proteins. Biochemistry. 1996 Jun 18; 35(24):7819-33. PMID: 8672483.
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    498. Elamrani S, Berry MB, Phillips GN, McCammon JA. Study of global motions in proteins by weighted masses molecular dynamics: adenylate kinase as a test case. Proteins. 1996 May; 25(1):79-88. PMID: 8727320.
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    499. Marrone TJ, Straatsma TP, Briggs JM, Wilson DK, Quiocho FA, McCammon JA. Theoretical study of inhibition of adenosine deaminase by (8R)-coformycin and (8R)-deoxycoformycin. J Med Chem. 1996 Jan 05; 39(1):277-84. PMID: 8568817.
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    500. Wlodek ST, Antosiewicz J, McCammon JA, Straatsma TP, Gilson MK, Briggs JM, Humblet C, Sussman JL. Binding of tacrine and 6-chlorotacrine by acetylcholinesterase. Biopolymers. 1996 Jan; 38(1):109-17. PMID: 8679940.
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    501. Antosiewicz J, Briggs JM, McCammon JA. Orientational steering in enzyme-substrate association: ionic strength dependence of hydrodynamic torque effects. Eur Biophys J. 1996; 24(3):137-41. PMID: 8852560.
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    502. Antosiewicz J, McCammon JA. Electrostatic and hydrodynamic orientational steering effects in enzyme-substrate association. Biophys J. 1995 Jul; 69(1):57-65. PMID: 7669910.
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    503. Pomès R, Willson RC, McCammon JA. Free energy simulations of the HyHEL-10/HEL antibody-antigen complex. Protein Eng. 1995 Jul; 8(7):663-75. PMID: 8577695.
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    504. Antosiewicz J, McCammon JA, Wlodek ST, Gilson MK. Simulation of charge-mutant acetylcholinesterases. Biochemistry. 1995 Apr 04; 34(13):4211-9. PMID: 7703233.
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    505. Cannon WR, Briggs JM, Shen J, McCammon JA, Quiocho FA. Conservative and nonconservative mutations in proteins: anomalous mutations in a transport receptor analyzed by free energy and quantum chemical calculations. Protein Sci. 1995 Mar; 4(3):387-93. PMID: 7795522.
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    506. Antosiewicz J, Gilson MK, Lee IH, McCammon JA. Acetylcholinesterase: diffusional encounter rate constants for dumbbell models of ligand. Biophys J. 1995 Jan; 68(1):62-8. PMID: 7711269.
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    507. Antosiewicz J, McCammon JA, Gilson MK. Prediction of pH-dependent properties of proteins. J Mol Biol. 1994 May 06; 238(3):415-36. PMID: 8176733.
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    508. Zacharias M, Luty BA, Davis ME, McCammon JA. Combined conformational search and finite-difference Poisson-Boltzmann approach for flexible docking. Application to an operator mutation in the lambda repressor-operator complex. J Mol Biol. 1994 May 06; 238(3):455-65. PMID: 8176736.
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    509. Gilson MK, Straatsma TP, McCammon JA, Ripoll DR, Faerman CH, Axelsen PH, Silman I, Sussman JL. Open "back door" in a molecular dynamics simulation of acetylcholinesterase. Science. 1994 Mar 04; 263(5151):1276-8. PMID: 8122110.
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    510. Wade RC, Luty BA, Demchuk E, Madura JD, Davis ME, Briggs JM, McCammon JA. Simulation of enzyme-substrate encounter with gated active sites. Nat Struct Biol. 1994 Jan; 1(1):65-9. PMID: 7656010.
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    511. Lesyng B, McCammon JA. Molecular modeling methods. Basic techniques and challenging problems. Pharmacol Ther. 1993 Nov; 60(2):149-67. PMID: 7912833.
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    512. Zacharias M, Straatsma TP, McCammon JA, Quiocho FA. Inversion of receptor binding preferences by mutagenesis: free energy thermodynamic integration studies on sugar binding to L-arabinose binding proteins. Biochemistry. 1993 Jul 27; 32(29):7428-34. PMID: 8338840.
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    513. Tan RC, Truong TN, McCammon JA, Sussman JL. Acetylcholinesterase: electrostatic steering increases the rate of ligand binding. Biochemistry. 1993 Jan 19; 32(2):401-3. PMID: 8422348.
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    514. Wade RC, Davis ME, Luty BA, Madura JD, McCammon JA. Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme. Biophys J. 1993 Jan; 64(1):9-15. PMID: 8431552.
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    515. Zacharias M, Luty BA, Davis ME, McCammon JA. Poisson-Boltzmann analysis of the lambda repressor-operator interaction. Biophys J. 1992 Nov; 63(5):1280-5. PMID: 1477279.
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    516. Wade RC, McCammon JA. Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side-chain conformations. II. Calculation of free-energy differences by thermodynamic integration. J Mol Biol. 1992 Jun 05; 225(3):697-712. PMID: 1318384.
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    517. Wade RC, McCammon JA. Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side-chain conformation. I. Mapping the rotamers of residue 188 of viral protein 1. J Mol Biol. 1992 Jun 05; 225(3):679-96. PMID: 1318383.
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    518. Tanner JJ, Nell LJ, McCammon JA. Anti-insulin antibody structure and conformation. II. Molecular dynamics with explicit solvent. Biopolymers. 1992 Jan; 32(1):23-32. PMID: 1617146.
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    519. Nell LJ, McCammon JA, Subramaniam S. Anti-insulin antibody structure and conformation. I. Molecular modeling and mechanics of an insulin antibody. Biopolymers. 1992 Jan; 32(1):11-21. PMID: 1377513.
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    520. Chiu SW, Nicholson LK, Brenneman MT, Subramaniam S, Teng Q, McCammon JA, Cross TA, Jakobsson E. Molecular dynamics computations and solid state nuclear magnetic resonance of the gramicidin cation channel. Biophys J. 1991 Oct; 60(4):974-8. PMID: 1720680.
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    521. Chiu SW, Jakobsson E, Subramaniam S, McCammon JA. Time-correlation analysis of simulated water motion in flexible and rigid gramicidin channels. Biophys J. 1991 Jul; 60(1):273-85. PMID: 1715766.
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    522. Wade RC, Mazor MH, McCammon JA, Quiocho FA. A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins. Biopolymers. 1991 Jul; 31(8):919-31. PMID: 1782354.
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    523. Straatsma TP, McCammon JA. Theoretical calculations of relative affinities of binding. Methods Enzymol. 1991; 202:497-511. PMID: 1784186.
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    524. Zheng C, Wong CF, McCammon JA. Fluctuation of the solvent-accessible surface area of tuna ferrocytochrome c. Biopolymers. 1990 Dec; 29(14):1877-83. PMID: 2169921.
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    525. Sines JJ, Allison SA, McCammon JA. Point charge distributions and electrostatic steering in enzyme/substrate encounter: Brownian dynamics of modified copper/zinc superoxide dismutases. Biochemistry. 1990 Oct 09; 29(40):9403-12. PMID: 2248953.
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    526. Shen J, Subramaniam S, Wong CF, McCammon JA. Superoxide dismutase: fluctuations in the structure and solvation of the active site channel studied by molecular dynamics simulation. Biopolymers. 1989 Dec; 28(12):2085-96. PMID: 2605312.
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    527. Chiu SW, Subramaniam S, Jakobsson E, McCammon JA. Water and polypeptide conformations in the gramicidin channel. A molecular dynamics study. Biophys J. 1989 Aug; 56(2):253-61. PMID: 2476188.
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    528. Jordan PC, Bacquet RJ, McCammon JA, Tran P. How electrolyte shielding influences the electrical potential in transmembrane ion channels. Biophys J. 1989 Jun; 55(6):1041-52. PMID: 2475181.
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    529. Lybrand TP, McCammon JA. Computer simulation study of the binding of an antiviral agent to a sensitive and a resistant human rhinovirus. J Comput Aided Mol Des. 1989 Jan; 2(4):259-66. PMID: 2541225.
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    530. Zheng C, Wong CF, McCammon JA, Wolynes PG. Quantum simulation of ferrocytochrome c. Nature. 1988 Aug 25; 334(6184):726-8. PMID: 2842687.
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    531. Allison SA, Bacquet RJ, McCammon JA. Simulation of the diffusion-controlled reaction between superoxide and superoxide dismutase. II. Detailed models. Biopolymers. 1988 Feb; 27(2):251-69. PMID: 2833950.
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    532. Wilcox GL, Quiocho FA, Levinthal C, Harvey SC, Maggiora GM, McCammon JA. Symposium overview. Minnesota Conference on Supercomputing in Biology: Proteins, Nucleic Acids, and Water. J Comput Aided Mol Des. 1988 Jan; 1(4):271-81. PMID: 3193133.
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    533. McCammon JA. Computer-aided molecular design. Science. 1987 Oct 23; 238(4826):486-91. PMID: 3310236.
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    534. Ghosh I, McCammon JA. Sidechain rotational isomerization in proteins. Dynamic simulation with solvent surroundings. Biophys J. 1987 Apr; 51(4):637-41. PMID: 3580489.
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    535. Bruccoleri RE, Karplus M, McCammon JA. The hinge-bending mode of a lysozyme-inhibitor complex. Biopolymers. 1986 Sep; 25(9):1767-802. PMID: 3768485.
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    536. Karplus M, McCammon JA. The dynamics of proteins. Sci Am. 1986 Apr; 254(4):42-51. PMID: 2938253.
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    537. Lybrand TP, McCammon JA, Wipff G. Theoretical calculation of relative binding affinity in host-guest systems. Proc Natl Acad Sci U S A. 1986 Feb; 83(4):833-5. PMID: 3456569.
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    538. Allison SA, Northrup SH, McCammon JA. Simulation of biomolecular diffusion and complex formation. Biophys J. 1986 Jan; 49(1):167-75. PMID: 3955168.
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    539. Bacquet RJ, McCammon JA. Salt effects on enzyme-substrate interactions by Monte Carlo simulation. Ann N Y Acad Sci. 1986; 482:245-7. PMID: 3471108.
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    540. Case DA, McCammon JA. Dynamic simulations of oxygen binding to myoglobin. Ann N Y Acad Sci. 1986; 482:222-33. PMID: 3471106.
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    541. Harvey SC, Prabhakaran M, McCammon JA. Molecular-dynamics simulation of phenylalanine transfer RNA. I. Methods and general results. Biopolymers. 1985 Jul; 24(7):1169-88. PMID: 3896333.
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    542. Prabhakaran M, Harvey SC, McCammon JA. Molecular-dynamics simulation of phenylalanine transfer RNA. II. Amplitudes, anisotropies, and anharmonicities of atomic motions. Biopolymers. 1985 Jul; 24(7):1189-204. PMID: 2992621.
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    543. Allison SA, Ganti G, McCammon JA. Simulation of the diffusion-controlled reaction between superoxide and superoxide dismutase. I. Simple models. Biopolymers. 1985 Jul; 24(7):1323-36. PMID: 2992623.
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    544. Prabhakaran M, McCammon JA, Harvey SC. Atomic motions in phenylalanine transfer RNA probed by molecular dynamics simulations. Prog Clin Biol Res. 1985; 172A:123-9. PMID: 3846288.
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    545. Tung CS, Harvey SC, McCammon JA. Large-amplitude bending motions in phenylalanine transfer RNA. Biopolymers. 1984 Nov; 23(11 Pt 1):2173-93. PMID: 6568122.
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    546. Levy RM, Srinivasan AR, Olson WK, McCammon JA. Quasi-harmonic method for studying very low frequency modes in proteins. Biopolymers. 1984 Jun; 23(6):1099-112. PMID: 6733249.
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    547. Harvey SC, Prabhakaran M, Mao B, McCammon JA. Phenylalanine transfer RNA: molecular dynamics simulation. Science. 1984 Mar 16; 223(4641):1189-91. PMID: 6560785.
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    548. Allison SA, McCammon JA. Multistep Brownian dynamics: application to short wormlike chains. Biopolymers. 1984 Feb; 23(2):363-75. PMID: 6704493.
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    549. Mao B, McCammon JA. Theoretical study of hinge bending in L-arabinose-binding protein. Internal energy and free energy changes. J Biol Chem. 1983 Oct 25; 258(20):12543-7. PMID: 6355087.
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    550. Karplus M, McCammon JA. Dynamics of proteins: elements and function. Annu Rev Biochem. 1983; 52:263-300. PMID: 6351724.
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    551. Mao B, Pear MR, McCammon JA, Northrup SH. Molecular dynamics of ferrocytochrome c: anharmonicity of atomic displacements. Biopolymers. 1982 Oct; 21(10):1979-89. PMID: 6293599.
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    552. Northrup SH, Pear MR, Lee CY, McCammon JA, Karplus M. Dynamical theory of activated processes in globular proteins. Proc Natl Acad Sci U S A. 1982 Jul; 79(13):4035-9. PMID: 6955788.
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    553. Mao B, Pear MR, McCammon JA, Quiocho FA. Hinge-bending in L-arabinose-binding protein. The "Venus's-flytrap" model. J Biol Chem. 1982 Feb 10; 257(3):1131-3. PMID: 7035444.
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    554. Northrup SH, Pear MR, Morgan JD, McCammon JA, Karplus M. Molecular dynamics of ferrocytochrome c. Magnitude and anisotropy of atomic displacements. J Mol Biol. 1981 Dec 25; 153(4):1087-109. PMID: 6283085.
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    555. Harvey SC, McCammon JA. Intramolecular flexibility in phenylalanine transfer RNA. Nature. 1981 Nov 19; 294(5838):286-7. PMID: 7029310.
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    556. McCammon JA, Northrup SH. Gated binding of ligands to proteins. Nature. 1981 Sep 24; 293(5830):316-7. PMID: 7278989.
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    557. Karplus M, McCammon JA. The internal dynamics of globular proteins. CRC Crit Rev Biochem. 1981; 9(4):293-349. PMID: 7009056.
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    558. Habibzadeh MA. Idiopathic hypertrophic subaortic stenosis and aortic regurgitation in an 84-year-old man. J Am Geriatr Soc. 1980 Nov; 28(11):515-8. PMID: 6107314.
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    559. Northrup SH, Pear MR, McCammon JA, Karplus M, Takano T. Internal mobility of ferrocytochrome c. Nature. 1980 Oct 16; 287(5783):659-60. PMID: 6253809.
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    560. Levy RM, Karplus M, McCammon JA. Molecular dynamics studies of NMR relaxation in proteins. Biophys J. 1980 Oct; 32(1):628-30. PMID: 19431400.
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    561. Karplus M, Gelin BR, McCammon JA. Internal dynamics of proteins. Short time and long time motions of aromatic sidechains in PTI. Biophys J. 1980 Oct; 32(1):603-18. PMID: 7248464.
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    562. Northrup SH, Pear MR, McCammon JA, Karplus M. Molecular dynamics of ferrocytochrome c. Nature. 1980 Jul 17; 286(5770):304-5. PMID: 6250059.
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    563. Northrup SH, McCammon JA. Simulation methods for protein structure fluctuations. Biopolymers. 1980 May; 19(5):1001-16. PMID: 7378544.
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    564. McCammon JA, Karplus M. Dynamics of activated processes in globular proteins. Proc Natl Acad Sci U S A. 1979 Aug; 76(8):3585-9. PMID: 291026.
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    565. McCammon JA, Wolynes PG, Karplus M. Picosecond dynamics of tyrosine side chains in proteins. Biochemistry. 1979 Mar 20; 18(6):927-42. PMID: 427100.
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    566. Karplus M, McCammon JA. Protein structural fluctuations during a period of 100 ps. Nature. 1979 Feb 15; 277(5697):578. PMID: 763343.
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    567. McCammon JA, Karplus M. Internal motions of antibody molecules. Nature. 1977 Aug 25; 268(5622):765-6. PMID: 895880.
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    568. McCammon JA, Gelin BR, Karplus M. Dynamics of folded proteins. Nature. 1977 Jun 16; 267(5612):585-90. PMID: 301613.
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    569. McCammon JA, Gelin BR, Karplus M, Wolynes PG. The hinge-bending mode in lysozyme. Nature. 1976 Jul 22; 262(5566):325-6. PMID: 958384.
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    570. McCammon JA, Deutch JM. Frictional properties of nonspherical multisubunit structures. Application to tubules and cylinders. Biopolymers. 1976 Jul; 15(7):1397-408. PMID: 949541.
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    571. McCammon JA, Deutch JM. "Semiempirical" models for biomembrane phase transitions and phase separations. J Am Chem Soc. 1975 Nov 12; 97(23):6675-81. PMID: 1184878.
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