James Mccammon

Title(s)Distinguished Professor of the Graduate Division, Chemistry and Biochemistry
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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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 Kansas2021Newmark 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 Interactions in Natural Product Biosynthesis
    NIH R01GM095970Mar 1, 2012 - Jan 31, 2024
    Role: Principal Investigator
    Theory of Biomolecular Diffusion
    NIH/NIGMS R01GM031479Jun 1, 1983 - Jun 30, 2023
    Role: Principal Investigator

    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. to make corrections and additions.
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    1. Multiscale Simulations Examining Glycan Shield Effects on Drug Binding to Influenza Neuraminidase. Biophys J. 2020 12 01; 119(11):2275-2289. Seitz C, Casalino L, Konecny R, Huber G, Amaro RE, McCammon JA. PMID: 33130120.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    2. Predicting the effects of dATP on cardiac contraction using multiscale modeling of the sarcomere. Arch Biochem Biophys. 2020 11 30; 695:108582. McCabe KJ, Aboelkassem Y, Teitgen AE, Huber GA, McCammon JA, Regnier M, McCulloch AD. PMID: 32956632.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    3. Interfacial plasticity facilitates high reaction rate of E. coli FAS malonyl-CoA:ACP transacylase, FabD. Proc Natl Acad Sci U S A. 2020 09 29; 117(39):24224-24233. Misson LE, Mindrebo JT, Davis TD, Patel A, McCammon JA, Noel JP, Burkart MD. PMID: 32929027.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    4. Elucidation of cryptic and allosteric pockets within the SARS-CoV-2 protease. bioRxiv. 2020 Jul 24. Sztain T, Amaro R, McCammon JA. PMID: 32743587.
      View in: PubMed   Mentions:
    5. Gating mechanism of elongating ß-ketoacyl-ACP synthases. Nat Commun. 2020 04 07; 11(1):1727. Mindrebo JT, Patel A, Kim WE, Davis TD, Chen A, Bartholow TG, La Clair JJ, McCammon JA, Noel JP, Burkart MD. PMID: 32265440.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    6. 3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries. PLoS Comput Biol. 2020 04; 16(4):e1007756. Lee CT, Laughlin JG, Angliviel de La Beaumelle N, Amaro RE, McCammon JA, Ramamoorthi R, Holst M, Rangamani P. PMID: 32251448.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    7. An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries. Biophys J. 2020 03 10; 118(5):1003-1008. Lee CT, Laughlin JG, Moody JB, Amaro RE, McCammon JA, Holst M, Rangamani P. PMID: 32032503.
      View in: PubMed   Mentions: 2     Fields:    
    8. Brownian Dynamics Simulations of Biological Molecules. Trends Chem. 2019 Nov; 1(8):727-738. Huber GA, McCammon JA. PMID: 32309795.
      View in: PubMed   Mentions:
    9. Shifting the Hydrolysis Equilibrium of Substrate Loaded Acyl Carrier Proteins. Biochemistry. 2019 08 27; 58(34):3557-3560. Sztain T, Bartholow TG, McCammon JA, Burkart MD. PMID: 31397556.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    10. A Stochastic Multiscale Model of Cardiac Thin Filament Activation Using Brownian-Langevin Dynamics. Biophys J. 2019 12 17; 117(12):2255-2272. Aboelkassem Y, McCabe KJ, Huber GA, Regnier M, McCammon JA, McCulloch AD. PMID: 31547973.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    11. The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation. ACM Trans Math Softw. 2019 Aug; 45(3). Lee CT, Moody JB, Amaro RE, McCammon JA, Holst MJ. PMID: 31474782.
      View in: PubMed   Mentions:
    12. Modifying the Thioester Linkage Affects the Structure of the Acyl Carrier Protein. Angew Chem Int Ed Engl. 2019 08 05; 58(32):10888-10892. Sztain T, Patel A, Lee DJ, Davis TD, McCammon JA, Burkart MD. PMID: 31140212.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    13. 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. Dodge GJ, Patel A, Jaremko KL, McCammon JA, Smith JL, Burkart MD. PMID: 30872475.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    14. Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics. ACS Cent Sci. 2019 Apr 24; 5(4):651-662. Ricci CG, Chen JS, Miao Y, Jinek M, Doudna JA, McCammon JA, Palermo G. PMID: 31041385.
      View in: PubMed   Mentions:
    15. Docking simulation and antibiotic discovery targeting the MlaC protein in Gram-negative bacteria. Chem Biol Drug Des. 2019 04; 93(4):647-652. Huang YM, Munguia J, Miao Y, Nizet V, McCammon JA. PMID: 30570806.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    16. Allostery in Its Many Disguises: From Theory to Applications. Structure. 2019 04 02; 27(4):566-578. 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. PMID: 30744993.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansAnimalsCells
    17. Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant. Biophys J. 2019 01 22; 116(2):205-214. Feher VA, Schiffer JM, Mermelstein DJ, Mih N, Pierce LCT, McCammon JA, Amaro RE. PMID: 30606449.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    18. Mechanistic Probes for the Epimerization Domain of Nonribosomal Peptide Synthetases. Chembiochem. 2019 01 18; 20(2):147-152. Kim WE, Patel A, Hur GH, Tufar P, Wuo MG, McCammon JA, Burkart MD. PMID: 30194895.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    19. Heterogeneous Solvation in Distinctive Protein-Protein Interfaces Revealed by Molecular Dynamics Simulations. J Phys Chem B. 2018 12 13; 122(49):11695-11701. Ricci CG, McCammon JA. PMID: 30252476.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    20. 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. Zhang J, Wang N, Miao Y, Hauser F, McCammon JA, Rappel WJ, Schroeder JI. PMID: 30301791.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    21. 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). Utesch T, de Miguel Catalina A, Schattenberg C, Paege N, Schmieder P, Krause E, Miao Y, McCammon JA, Meyer V, Jung S, Mroginski MA. PMID: 30282755.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    22. pH-dependent conformational dynamics of beta-secretase 1: A molecular dynamics study. J Mol Recognit. 2019 03; 32(3):e2765. Mermelstein DJ, McCammon JA, Walker RC. PMID: 30264484.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    23. Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain. Q Rev Biophys. 2018; 51. Palermo G, Chen JS, Ricci CG, Rivalta I, Jinek M, Batista VS, Doudna JA, McCammon JA. PMID: 30555184.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    24. Ensemble Docking in Drug Discovery. Biophys J. 2018 05 22; 114(10):2271-2278. Amaro RE, Baudry J, Chodera J, Demir Ö, McCammon JA, Miao Y, Smith JC. PMID: 29606412.
      View in: PubMed   Mentions: 62     Fields:    Translation:Cells
    25. Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package. J Comput Chem. 2018 07 15; 39(19):1354-1358. Mermelstein DJ, Lin C, Nelson G, Kretsch R, McCammon JA, Walker RC. PMID: 29532496.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    26. Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation. J Chem Theory Comput. 2018 Apr 10; 14(4):1853-1864. Huang YM, McCammon JA, Miao Y. PMID: 29489349.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    27. 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. Miao Y, McCammon JA. PMID: 29507218.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    28. Membrane Allostery and Unique Hydrophobic Sites Promote Enzyme Substrate Specificity. J Am Chem Soc. 2018 03 07; 140(9):3285-3291. Mouchlis VD, Chen Y, McCammon JA, Dennis EA. PMID: 29342349.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    29. RPYFMM: Parallel Adaptive Fast Multipole Method for Rotne-Prager-Yamakawa Tensor in Biomolecular Hydrodynamics Simulations. Comput Phys Commun. 2018 Jun; 227:99-108. Guan W, Cheng X, Huang J, Huber G, Li W, McCammon JA, Zhang B. PMID: 30147116.
      View in: PubMed   Mentions:
    30. Ligand Binding Pathways and Conformational Transitions of the HIV Protease. Biochemistry. 2018 03 06; 57(9):1533-1541. Miao Y, Huang YM, Walker RC, McCammon JA, Chang CA. PMID: 29394043.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    31. Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly. Front Mol Biosci. 2018; 5:13. Ricci CG, Li B, Cheng LT, Dzubiella J, McCammon JA. PMID: 29484300.
      View in: PubMed   Mentions:
    32. Remarkable similarity in Plasmodium falciparum and Plasmodium vivax geranylgeranyl diphosphate synthase dynamics and its implication for antimalarial drug design. Chem Biol Drug Des. 2018 06; 91(6):1068-1077. Venkatramani A, Gravina Ricci C, Oldfield E, McCammon JA. PMID: 29345110.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    33. Brownian dynamic study of an enzyme metabolon in the TCA cycle: Substrate kinetics and channeling. Protein Sci. 2018 02; 27(2):463-471. Huang YM, Huber GA, Wang N, Minteer SD, McCammon JA. PMID: 29094409.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    34. Improvements to the APBS biomolecular solvation software suite. Protein Sci. 2018 01; 27(1):112-128. 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. PMID: 28836357.
      View in: PubMed   Mentions: 191     Fields:    
    35. Manipulating Protein-Protein Interactions in Nonribosomal Peptide Synthetase Type II Peptidyl Carrier Proteins. Biochemistry. 2017 10 10; 56(40):5269-5273. Jaremko MJ, Lee DJ, Patel A, Winslow V, Opella SJ, McCammon JA, Burkart MD. PMID: 28920687.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    36. Protospacer Adjacent Motif-Induced Allostery Activates CRISPR-Cas9. J Am Chem Soc. 2017 11 15; 139(45):16028-16031. Palermo G, Ricci CG, Fernando A, Basak R, Jinek M, Rivalta I, Batista VS, McCammon JA. PMID: 28764328.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    37. Mapping the allosteric sites of the A2A adenosine receptor. Chem Biol Drug Des. 2018 01; 91(1):5-16. Caliman AD, Miao Y, McCammon JA. PMID: 28639411.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    38. "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. Ricci CG, Li B, Cheng LT, Dzubiella J, McCammon JA. PMID: 28613904.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    39. CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Proc Natl Acad Sci U S A. 2017 07 11; 114(28):7260-7265. Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. PMID: 28652374.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    40. Activation mechanisms of the first sphingosine-1-phosphate receptor. Protein Sci. 2017 06; 26(6):1150-1160. Caliman AD, Miao Y, McCammon JA. PMID: 28370663.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    41. Spectroscopic and Computational Investigations of Ligand Binding to IspH: Discovery of Non-diphosphate Inhibitors. Chembiochem. 2017 05 18; 18(10):914-920. O'Dowd B, Williams S, Wang H, No JH, Rao G, Wang W, McCammon JA, Cramer SP, Oldfield E. PMID: 28253432.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    42. Effect of donor atom identity on metal-binding pharmacophore coordination. J Biol Inorg Chem. 2017 Jun; 22(4):605-613. Dick BL, Patel A, McCammon JA, Cohen SM. PMID: 28389830.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    43. NMR structure-based optimization of Staphylococcus aureus sortase A pyridazinone inhibitors. Chem Biol Drug Des. 2017 Sep; 90(3):327-344. 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. PMID: 28160417.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    44. Gaussian Accelerated Molecular Dynamics in NAMD. J Chem Theory Comput. 2017 01 10; 13(1):9-19. Pang YT, Miao Y, Wang Y, McCammon JA. PMID: 28034310.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    45. 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. Miao Y, McCammon JA. PMID: 27791003.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansCells
    46. 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. Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. PMID: 27800559.
      View in: PubMed   Mentions:
    47. 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. Miao Y, Goldfeld DA, Moo EV, Sexton PM, Christopoulos A, McCammon JA, Valant C. PMID: 27601651.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    48. Dynamic Structure and Inhibition of a Malaria Drug Target: Geranylgeranyl Diphosphate Synthase. Biochemistry. 2016 09 13; 55(36):5180-90. G Ricci C, Liu YL, Zhang Y, Wang Y, Zhu W, Oldfield E, McCammon JA. PMID: 27564465.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    49. Autobiography of J. Andrew McCammon. J Phys Chem B. 2016 08 25; 120(33):8057-60. McCammon JA. PMID: 27558539.
      View in: PubMed   Mentions: 1     Fields:    
    50. Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations. J Chem Phys. 2016 Aug 07; 145(5):054114. Zhou S, Sun H, Cheng LT, Dzubiella J, Li B, McCammon JA. PMID: 27497546.
      View in: PubMed   Mentions: 1     Fields:    
    51. Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review. Mol Simul. 2016; 42(13):1046-1055. Miao Y, McCammon JA. PMID: 27453631.
      View in: PubMed   Mentions:
    52. G-protein coupled receptors: advances in simulation and drug discovery. Curr Opin Struct Biol. 2016 12; 41:83-89. Miao Y, McCammon JA. PMID: 27344006.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCells
    53. 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. Huang YM, Miao Y, Munguia J, Lin L, Nizet V, McCammon JA. PMID: 27111825.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    54. 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. Mouchlis VD, Morisseau C, Hammock BD, Li S, McCammon JA, Dennis EA. PMID: 27320659.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    55. Hybrid finite element and Brownian dynamics method for charged particles. J Chem Phys. 2016 Apr 28; 144(16):164107. Huber GA, Miao Y, Zhou S, Li B, McCammon JA. PMID: 27131531.
      View in: PubMed   Mentions:    Fields:    
    56. 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. Mouchlis VD, Limnios D, Kokotou MG, Barbayianni E, Kokotos G, McCammon JA, Dennis EA. PMID: 27087127.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    57. General trends of dihedral conformational transitions in a globular protein. Proteins. 2016 Apr; 84(4):501-14. Miao Y, Baudry J, Smith JC, McCammon JA. PMID: 26799251.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    58. Computation of pH-dependent binding free energies. Biopolymers. 2016 Jan; 105(1):43-9. Kim MO, McCammon JA. PMID: 26202905.
      View in: PubMed   Mentions: 5     Fields:    
    59. 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. Sun H, Wen J, Zhao Y, Li B, McCammon JA. PMID: 26723595.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    60. Antiinfectives targeting enzymes and the proton motive force. Proc Natl Acad Sci U S A. 2015 Dec 22; 112(51):E7073-82. 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. PMID: 26644565.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansCells
    61. Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor. Q Rev Biophys. 2015 Nov; 48(4):479-87. Kappel K, Miao Y, McCammon JA. PMID: 26537408.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansCells
    62. 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. Kim MO, Blachly PG, McCammon JA. PMID: 26506513.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    63. 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. Cheng Y, Rao V, Tu AY, Lindert S, Wang D, Oxenford L, McCulloch AD, McCammon JA, Regnier M. PMID: 26391394.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimalsCells
    64. Electrostatic steering enhances the rate of cAMP binding to phosphodiesterase: Brownian dynamics modeling. Protein Sci. 2015 Nov; 24(11):1884-9. Huang YM, Huber G, McCammon JA. PMID: 26346301.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    65. 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. Kekenes-Huskey PM, Eun C, McCammon JA. PMID: 26342355.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    66. Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation. J Chem Theory Comput. 2015 Aug 11; 11(8):3584-3595. Miao Y, Feher VA, McCammon JA. PMID: 26300708.
      View in: PubMed   Mentions: 107     Fields:    
    67. Substrate channeling between the human dihydrofolate reductase and thymidylate synthase. Protein Sci. 2016 Jan; 25(1):79-86. Wang N, McCammon JA. PMID: 26096018.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    68. 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. Blachly PG, Sandala GM, Giammona DA, Bashford D, McCammon JA, Noodleman L. PMID: 26098647.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    69. Accelerated molecular dynamics simulations of protein folding. J Comput Chem. 2015 Jul 30; 36(20):1536-49. Miao Y, Feixas F, Eun C, McCammon JA. PMID: 26096263.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    70. 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. Kaus JW, Harder E, Lin T, Abel R, McCammon JA, Wang L. PMID: 26085821.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    71. Enhanced ligand sampling for relative protein-ligand binding free energy calculations. J Phys Chem B. 2015 May 21; 119(20):6190-7. Kaus JW, McCammon JA. PMID: 25906170.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    72. Investigation of the conformational dynamics of the apo A2A adenosine receptor. Protein Sci. 2015 Jun; 24(6):1004-12. Caliman AD, Swift SE, Wang Y, Miao Y, McCammon JA. PMID: 25761901.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    73. 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. Miao Y, Caliman AD, McCammon JA. PMID: 25863070.
      View in: PubMed   Mentions: 31     Fields:    Translation:Cells
    74. 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. Kekenes-Huskey PM, Gillette AK, McCammon JA. PMID: 25770569.
      View in: PubMed   Mentions:    Fields:    
    75. LS-VISM: A software package for analysis of biomolecular solvation. J Comput Chem. 2015 May 30; 36(14):1047-59. Zhou S, Cheng LT, Sun H, Che J, Dzubiella J, Li B, McCammon JA. PMID: 25766844.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    76. 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. Lindert S, McCammon JA. PMID: 25883538.
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    77. 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. Guo Z, Li B, Cheng LT, Zhou S, McCammon JA, Che J. PMID: 25941465.
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    78. 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. Mouchlis VD, Bucher D, McCammon JA, Dennis EA. PMID: 25624474.
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    79. 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. Lindert S, Cheng Y, Kekenes-Huskey P, Regnier M, McCammon JA. PMID: 25606687.
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    80. Poisson-Boltzmann versus Size-Modified Poisson-Boltzmann Electrostatics Applied to Lipid Bilayers. J Phys Chem B. 2014 Dec 26; 118(51):14827-32. Wang N, Zhou S, Kekenes-Huskey PM, Li B, McCammon JA. PMID: 25426875.
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    81. 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. Kim MO, Feng X, Feixas F, Zhu W, Lindert S, Bogue S, Sinko W, de Oliveira C, Rao G, Oldfield E, McCammon JA. PMID: 25352216.
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    82. Electrostatic channeling in P. falciparum DHFR-TS: Brownian dynamics and Smoluchowski modeling. Biophys J. 2014 Nov 18; 107(10):2394-402. Metzger VT, Eun C, Kekenes-Huskey PM, Huber G, McCammon JA. PMID: 25418308.
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    83. 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. Bertolini R, Goepfert C, Andrieu T, Nichols S, Walter MA, Frey FJ, McCammon JA, Frey BM. PMID: 25358634.
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    84. In silico screening for Plasmodium falciparum enoyl-ACP reductase inhibitors. J Comput Aided Mol Des. 2015 Jan; 29(1):79-87. Lindert S, Tallorin L, Nguyen QG, Burkart MD, McCammon JA. PMID: 25344312.
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    85. 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. Cheng Y, Lindert S, Kekenes-Huskey P, Rao VS, Solaro RJ, Rosevear PR, Amaro R, McCulloch AD, McCammon JA, Regnier M. PMID: 25296321.
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    86. Celastrol inhibits Plasmodium falciparum enoyl-acyl carrier protein reductase. Bioorg Med Chem. 2014 Nov 01; 22(21):6053-6061. Tallorin LC, Durrant JD, Nguyen QG, McCammon JA, Burkart MD. PMID: 25284249.
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    87. PKA phosphorylation of cardiac troponin I modulates activation and relaxation kinetics of ventricular myofibrils. Biophys J. 2014 Sep 02; 107(5):1196-1204. Rao V, Cheng Y, Lindert S, Wang D, Oxenford L, McCulloch AD, McCammon JA, Regnier M. PMID: 25185555.
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    88. 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. Brown LM, Rogers KE, Aroonsakool N, McCammon JA, Insel PA. PMID: 25183009.
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    89. Protocols utilizing constant pH molecular dynamics to compute pH-dependent binding free energies. J Phys Chem B. 2015 Jan 22; 119(3):861-72. Kim MO, Blachly PG, Kaus JW, McCammon JA. PMID: 25134690.
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    90. Trypsinogen activation as observed in accelerated molecular dynamics simulations. Protein Sci. 2014 Nov; 23(11):1550-8. Boechi L, Pierce L, Komives EA, McCammon JA. PMID: 25131668.
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    91. Exploring the influence of the protein environment on metal-binding pharmacophores. J Med Chem. 2014 Aug 28; 57(16):7126-35. Martin DP, Blachly PG, McCammon JA, Cohen SM. PMID: 25116076.
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    92. 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. Blachly PG, Sandala GM, Giammona DA, Liu T, Bashford D, McCammon JA, Noodleman L. PMID: 25221444.
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    93. Computer-aided drug discovery approach finds calcium sensitizer of cardiac troponin. Chem Biol Drug Des. 2015 Feb; 85(2):99-106. Lindert S, Li MX, Sykes BD, McCammon JA. PMID: 24954187.
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    94. Special Issue on Free Energy. J Chem Theory Comput. 2014 Jul 08; 10(7):2631. McCammon JA, Roux B, Voth G, Yang W. PMID: 26586502.
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    95. Undecaprenyl diphosphate synthase inhibitors: antibacterial drug leads. J Med Chem. 2014 Jul 10; 57(13):5693-701. Sinko W, Wang Y, Zhu W, Zhang Y, Feixas F, Cox CL, Mitchell DA, Oldfield E, McCammon JA. PMID: 24827744.
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    96. 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. Liu YL, Lindert S, Zhu W, Wang K, McCammon JA, Oldfield E. PMID: 24927548.
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    97. 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. Eun C, Ortiz-Sánchez JM, Da L, Wang D, McCammon JA. PMID: 24842057.
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    98. Accelerated adaptive integration method. J Phys Chem B. 2014 May 15; 118(19):5109-18. Kaus JW, Arrar M, McCammon JA. PMID: 24780083.
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    99. Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation. J Chem Theory Comput. 2014 Jul 08; 10(7):2677-2689. Miao Y, Sinko W, Pierce L, Bucher D, Walker RC, McCammon JA. PMID: 25061441.
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    100. 'Unconventional' coordination chemistry by metal chelating fragments in a metalloprotein active site. J Am Chem Soc. 2014 Apr 09; 136(14):5400-6. Martin DP, Blachly PG, Marts AR, Woodruff TM, de Oliveira CA, McCammon JA, Tierney DL, Cohen SM. PMID: 24635441.
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    101. 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. Ivetac A, Swift SE, Boyer PL, Diaz A, Naughton J, Young JA, Hughes SH, McCammon JA. PMID: 24405985.
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    102. A model study of sequential enzyme reactions and electrostatic channeling. J Chem Phys. 2014 Mar 14; 140(10):105101. Eun C, Kekenes-Huskey PM, Metzger VT, McCammon JA. PMID: 24628210.
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    103. Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields. J Chem Theory Comput. 2014 Apr 08; 10(4):1631-1637. Götz AW, Bucher D, Lindert S, McCammon JA. PMID: 24803868.
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    104. Variational Implicit Solvation with Poisson-Boltzmann Theory. J Chem Theory Comput. 2014 Apr 08; 10(4):1454-1467. Zhou S, Cheng LT, Dzubiella J, Li B, McCammon JA. PMID: 24803864.
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    105. 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. Jacobitz AW, Wereszczynski J, Yi SW, Amer BR, Huang GL, Nguyen AV, Sawaya MR, Jung ME, McCammon JA, Clubb RT. PMID: 24519933.
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    106. 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. Lindert S, Maslennikov I, Chiu EJ, Pierce LC, McCammon JA, Choe S. PMID: 24525125.
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    107. 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. Brown LM, Rogers KE, McCammon JA, Insel PA. PMID: 24497631.
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    108. Heterogeneous Hydration of p53/MDM2 Complex. J Chem Theory Comput. 2014 Mar 11; 10(3):1302-1313. Guo Z, Li B, Dzubiella J, Cheng LT, McCammon JA, Che J. PMID: 24803860.
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    109. Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics. Phys Chem Chem Phys. 2014 Apr 14; 16(14):6398-406. Miao Y, Nichols SE, McCammon JA. PMID: 24445284.
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    110. 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. Miller B, Friedman AJ, Choi H, Hogan J, McCammon JA, Hook V, Gerwick WH. PMID: 24364476.
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    111. Trapping the dynamic acyl carrier protein in fatty acid biosynthesis. Nature. 2014 Jan 16; 505(7483):427-31. 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. PMID: 24362570.
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    112. Utilizing a dynamical description of IspH to aid in the development of novel antimicrobial drugs. PLoS Comput Biol. 2013; 9(12):e1003395. Blachly PG, de Oliveira CA, Williams SL, McCammon JA. PMID: 24367248.
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    113. Exploring the role of receptor flexibility in structure-based drug discovery. Biophys Chem. 2014 Feb; 186:31-45. Feixas F, Lindert S, Sinko W, McCammon JA. PMID: 24332165.
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    114. Molecular and subcellular-scale modeling of nucleotide diffusion in the cardiac myofilament lattice. Biophys J. 2013 Nov 05; 105(9):2130-40. Kekenes-Huskey PM, Liao T, Gillette AK, Hake JE, Zhang Y, Michailova AP, McCulloch AD, McCammon JA. PMID: 24209858.
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    115. Mapping of allosteric druggable sites in activation-associated conformers of the M2 muscarinic receptor. Chem Biol Drug Des. 2014 Feb; 83(2):237-46. Miao Y, Nichols SE, McCammon JA. PMID: 24112716.
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    116. 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. Lindert S, Bucher D, Eastman P, Pande V, McCammon JA. PMID: 24634618.
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    117. 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. Chan AH, Wereszczynski J, Amer BR, Yi SW, Jung ME, McCammon JA, Clubb RT. PMID: 23701677.
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    118. Substrate-dependent dynamics of UDP-galactopyranose mutase: Implications for drug design. Protein Sci. 2013 Nov; 22(11):1490-501. Boechi L, de Oliveira CA, Da Fonseca I, Kizjakina K, Sobrado P, Tanner JJ, McCammon JA. PMID: 23934860.
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    119. Inactivating mutation in histone deacetylase 3 stabilizes its active conformation. Protein Sci. 2013 Oct; 22(10):1306-12. Arrar M, de Oliveira CA, McCammon JA. PMID: 23904210.
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    120. 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. Zhou S, Rogers KE, de Oliveira CA, Baron R, Cheng LT, Dzubiella J, Li B, McCammon JA. PMID: 24039554.
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    121. Influence of neighboring reactive particles on diffusion-limited reactions. J Chem Phys. 2013 Jul 28; 139(4):044117. Eun C, Kekenes-Huskey PM, McCammon JA. PMID: 23901970.
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    122. 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. Bucher D, Hsu YH, Mouchlis VD, Dennis EA, McCammon JA. PMID: 23935474.
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    123. Phase-field approach to implicit solvation of biomolecules with Coulomb-field approximation. J Chem Phys. 2013 Jul 14; 139(2):024111. Zhao Y, Kwan YY, Che J, Li B, McCammon JA. PMID: 23862933.
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    124. Population based reweighting of scaled molecular dynamics. J Phys Chem B. 2013 Oct 24; 117(42):12759-68. Sinko W, Miao Y, de Oliveira CA, McCammon JA. PMID: 23721224.
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    125. 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. Durrant JD, Friedman AJ, Rogers KE, McCammon JA. PMID: 23734946.
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    126. Iterative Molecular Dynamics-Rosetta Protein Structure Refinement Protocol to Improve Model Quality. J Chem Theory Comput. 2013 Aug 13; 9(8):3843-3847. Lindert S, Meiler J, McCammon JA. PMID: 23956701.
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    127. Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes. Mol Based Math Biol. 2013 Jul; 1. Liao T, Zhang Y, Kekenes-Huskey PM, Cheng Y, Michailova A, McCulloch AD, Holst M, McCammon JA. PMID: 24352481.
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    128. Activation and dynamic network of the M2 muscarinic receptor. Proc Natl Acad Sci U S A. 2013 Jul 02; 110(27):10982-7. Miao Y, Nichols SE, Gasper PM, Metzger VT, McCammon JA. PMID: 23781107.
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    129. Farnesyl diphosphate synthase inhibitors from in silico screening. Chem Biol Drug Des. 2013 Jun; 81(6):742-8. Lindert S, Zhu W, Liu YL, Pang R, Oldfield E, McCammon JA. PMID: 23421555.
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    130. Correlated motions and residual frustration in thrombin. J Phys Chem B. 2013 Oct 24; 117(42):12857-63. Fuglestad B, Gasper PM, McCammon JA, Markwick PR, Komives EA. PMID: 23621631.
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    131. Assessing the two-body diffusion tensor calculated by the bead models. J Chem Phys. 2013 May 28; 138(20):204117. Wang N, Huber GA, McCammon JA. PMID: 23742464.
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    132. AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design. J Mol Graph Model. 2013 Jul; 44:104-12. Durrant JD, Lindert S, McCammon JA. PMID: 23792207.
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    133. Structure-based network analysis of an evolved G protein-coupled receptor homodimer interface. Protein Sci. 2013 Jun; 22(6):745-54. Nichols SE, Hernández CX, Wang Y, McCammon JA. PMID: 23553730.
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    134. 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. Kim MO, Nichols SE, Wang Y, McCammon JA. PMID: 23579613.
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    135. Molecular recognition and ligand association. Annu Rev Phys Chem. 2013; 64:151-75. Baron R, McCammon JA. PMID: 23473376.
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    136. 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. Guerry P, Salmon L, Mollica L, Ortega Roldan JL, Markwick P, van Nuland NA, McCammon JA, Blackledge M. PMID: 23371543.
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    137. 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. Guo Z, Li B, Dzubiella J, Cheng LT, McCammon JA, Che J. PMID: 23505345.
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    138. 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. Hsu YH, Bucher D, Cao J, Li S, Yang SW, Kokotos G, Woods VL, McCammon JA, Dennis EA. PMID: 23256506.
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    139. Solvent fluctuations in hydrophobic cavity-ligand binding kinetics. Proc Natl Acad Sci U S A. 2013 Jan 22; 110(4):1197-202. Setny P, Baron R, Michael Kekenes-Huskey P, McCammon JA, Dzubiella J. PMID: 23297241.
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    140. Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design. Chem Biol Drug Des. 2013 Jan; 81(1):41-9. Sinko W, Lindert S, McCammon JA. PMID: 23253130.
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    141. Antibacterial drug leads targeting isoprenoid biosynthesis. Proc Natl Acad Sci U S A. 2013 Jan 02; 110(1):123-8. 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. PMID: 23248302.
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    142. 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. Arrar M, de Oliveira CA, Fajer M, Sinko W, McCammon JA. PMID: 23316122.
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    143. 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. Kappel K, Wereszczynski J, Clubb RT, McCammon JA. PMID: 23023444.
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    144. 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. Kekenes-Huskey PM, Lindert S, McCammon JA. PMID: 23209387.
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    145. 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. Arrar M, Turnham R, Pierce L, de Oliveira CA, McCammon JA. PMID: 23139175.
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    146. Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities. Proc Natl Acad Sci U S A. 2012 Dec 26; 109(52):21216-22. Gasper PM, Fuglestad B, Komives EA, Markwick PR, McCammon JA. PMID: 23197839.
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    147. 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. Kekenes-Huskey PM, Gillette A, Hake J, McCammon JA. PMID: 23293662.
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    148. On the Role of Dewetting Transitions in Host-Guest Binding Free Energy Calculations. J Chem Theory Comput. 2013 Jan 08; 9(1):46-53. Rogers KE, Ortiz-Sánchez JM, Baron R, Fajer M, de Oliveira CA, McCammon JA. PMID: 23316123.
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    149. 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. Lindert S, Kekenes-Huskey PM, McCammon JA. PMID: 23083722.
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    150. Dynamics of Plasmodium falciparum enoyl-ACP reductase and implications on drug discovery. Protein Sci. 2012 Nov; 21(11):1734-45. Lindert S, McCammon JA. PMID: 22969045.
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    151. 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. Kekenes-Huskey PM, Cheng Y, Hake JE, Sachse FB, Bridge JH, Holst MJ, McCammon JA, McCulloch AD, Michailova AP. PMID: 23060801.
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    152. Spectroscopic and computational study of melittin, cecropin A, and the hybrid peptide CM15. J Phys Chem B. 2012 Sep 06; 116(35):10600-8. Schlamadinger DE, Wang Y, McCammon JA, Kim JE. PMID: 22845179.
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    153. Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics. J Chem Theory Comput. 2012 Sep 11; 8(9):2997-3002. Pierce LC, Salomon-Ferrer R, Augusto F de Oliveira C, McCammon JA, Walker RC. PMID: 22984356.
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    154. iAPBS: a programming interface to Adaptive Poisson-Boltzmann Solver (APBS). Comput Sci Discov. 2012 Jul 26; 5(1). Konecny R, Baker NA, McCammon JA. PMID: 22905037.
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    155. Identification of potential small molecule binding pockets on Rho family GTPases. PLoS One. 2012; 7(7):e40809. Ortiz-Sanchez JM, Nichols SE, Sayyah J, Brown JH, McCammon JA, Grant BJ. PMID: 22815826.
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    156. The dynamic structure of thrombin in solution. Biophys J. 2012 Jul 03; 103(1):79-88. Fuglestad B, Gasper PM, Tonelli M, McCammon JA, Markwick PR, Komives EA. PMID: 22828334.
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    157. 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. Ortiz-Sánchez JM, Bucher D, Pierce LC, Markwick PR, McCammon JA. PMID: 22904696.
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    158. 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. Lindert S, Durrant JD, McCammon JA. PMID: 22594624.
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    159. Novel cruzain inhibitors for the treatment of Chagas' disease. Chem Biol Drug Des. 2012 Sep; 80(3):398-405. Rogers KE, Keränen H, Durrant JD, Ratnam J, Doak A, Arkin MR, McCammon JA. PMID: 22613098.
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    160. 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. Salmon L, Pierce L, Grimm A, Ortega Roldan JL, Mollica L, Jensen MR, van Nuland N, Markwick PR, McCammon JA, Blackledge M. PMID: 22565613.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    161. 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. Friedman AJ, Durrant JD, Pierce LC, McCorvie TJ, Timson DJ, McCammon JA. PMID: 22487100.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    162. 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. Wereszczynski J, McCammon JA. PMID: 22547793.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    163. Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions. J Chem Phys. 2012 Apr 28; 136(16):164107. Bauler P, Huber GA, McCammon JA. PMID: 22559470.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    164. Modelling cardiac calcium sparks in a three-dimensional reconstruction of a calcium release unit. J Physiol. 2012 Sep 15; 590(18):4403-22. Hake J, Edwards AG, Yu Z, Kekenes-Huskey PM, Michailova AP, McCammon JA, Holst MJ, Hoshijima M, McCulloch AD. PMID: 22495592.
      View in: PubMed   Mentions: 44     Fields:    Translation:AnimalsCells
    165. AutoClickChem: click chemistry in silico. PLoS Comput Biol. 2012; 8(3):e1002397. Durrant JD, McCammon JA. PMID: 22438795.
      View in: PubMed   Mentions: 11     Fields:    
    166. Simulations of the p97 complex suggest novel conformational states of hydrolysis intermediates. Protein Sci. 2012 Apr; 21(4):475-86. Wereszczynski J, McCammon JA. PMID: 22238181.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    167. Comparative molecular dynamics simulations of the antimicrobial peptide CM15 in model lipid bilayers. Biochim Biophys Acta. 2012 May; 1818(5):1402-9. Wang Y, Schlamadinger DE, Kim JE, McCammon JA. PMID: 22387432.
      View in: PubMed   Mentions: 26     Fields:    Translation:Cells
    168. Thermodynamic integration to predict host-guest binding affinities. J Comput Aided Mol Des. 2012 May; 26(5):569-76. Lawrenz M, Wereszczynski J, Ortiz-Sánchez JM, Nichols SE, McCammon JA. PMID: 22350568.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    169. 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. Lindert S, Kekenes-Huskey PM, Huber G, Pierce L, McCammon JA. PMID: 22329450.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    170. Accelerated molecular dynamics in computational drug design. Methods Mol Biol. 2012; 819:515-24. Wereszczynski J, McCammon JA. PMID: 22183555.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    171. ADAPTIVE FINITE ELEMENT MODELING TECHNIQUES FOR THE POISSON-BOLTZMANN EQUATION. Commun Comput Phys. 2012; 11(1):179-214. Holst M, McCammon JA, Yu Z, Zhou Y, Zhu Y. PMID: 21949541.
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    172. Independent-Trajectory Thermodynamic Integration: a practical guide to protein-drug binding free energy calculations using distributed computing. Methods Mol Biol. 2012; 819:469-86. Lawrenz M, Baron R, Wang Y, McCammon JA. PMID: 22183552.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    173. On the use of molecular dynamics receptor conformations for virtual screening. Methods Mol Biol. 2012; 819:93-103. Nichols SE, Baron R, McCammon JA. PMID: 22183532.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    174. Guide to virtual screening: application to the Akt phosphatase PHLPP. Methods Mol Biol. 2012; 819:561-73. Sinko W, Sierecki E, de Oliveira CA, McCammon JA. PMID: 22183558.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    175. A molecular dynamics ensemble-based approach for the mapping of druggable binding sites. Methods Mol Biol. 2012; 819:3-12. Ivetac A, McCammon JA. PMID: 22183526.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    176. Level-Set Variational Implicit-Solvent Modeling of Biomolecules with the Coulomb-Field Approximation. J Chem Theory Comput. 2012 Feb 14; 8(2):386-397. Wang Z, Che J, Cheng LT, Dzubiella J, Li B, McCammon JA. PMID: 22346739.
      View in: PubMed   Mentions: 18     Fields:    
    177. Electrostatically biased binding of kinesin to microtubules. PLoS Biol. 2011 Nov; 9(11):e1001207. Grant BJ, Gheorghe DM, Zheng W, Alonso M, Huber G, Dlugosz M, McCammon JA, Cross RA. PMID: 22140358.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    178. 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. Sinko W, de Oliveira CA, Pierce LC, McCammon JA. PMID: 22241967.
      View in: PubMed   Mentions: 12     Fields:    
    179. Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition. Q Rev Biophys. 2012 Feb; 45(1):1-25. Wereszczynski J, McCammon JA. PMID: 22082669.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    180. Gated Diffusion-controlled Reactions. BMC Biophys. 2011 Mar 02; 4:4. McCammon JA. PMID: 21595999.
      View in: PubMed   Mentions:
    181. 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. Sander T, Frølund B, Bruun AT, Ivanov I, McCammon JA, Balle T. PMID: 21365676.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    182. 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. McCammon JA. PMID: 19416830.
      View in: PubMed   Mentions: 19     Fields:    Translation:AnimalsCells
    183. Target flexibility in molecular recognition. Biochim Biophys Acta. 2005 Dec 30; 1754(1-2):221-4. McCammon JA. PMID: 16181817.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    184. Theory of biomolecular recognition. Curr Opin Struct Biol. 1998 Apr; 8(2):245-9. McCammon JA. PMID: 9631300.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansAnimalsCells
    185. Idiopathic hypertrophic subaortic stenosis and aortic regurgitation in an 84-year-old man. J Am Geriatr Soc. 1980 Nov; 28(11):515-8. Habibzadeh MA. PMID: 6107314.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    186. Internal dynamics of proteins. Short time and long time motions of aromatic sidechains in PTI. Biophys J. 1980 Oct; 32(1):603-18. Karplus M, Gelin BR, McCammon JA. PMID: 7248464.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    187. Protein structural fluctuations during a period of 100 ps. Nature. 1979 Feb 15; 277(5697):578. Karplus M, McCammon JA. PMID: 763343.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    188. Frictional properties of nonspherical multisubunit structures. Application to tubules and cylinders. Biopolymers. 1976 Jul; 15(7):1397-408. McCammon JA, Deutch JM. PMID: 949541.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    189. "Semiempirical" models for biomembrane phase transitions and phase separations. J Am Chem Soc. 1975 Nov 12; 97(23):6675-81. McCammon JA, Deutch JM. PMID: 1184878.
      View in: PubMed   Mentions: 4     Fields:    
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