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James Mccammon

Title(s)Emeritus Professor, 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 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 Interactions in Natural Product Biosynthesis
    NIH/NIGMS R01GM095970Mar 1, 2012 - Jan 31, 2020
    Role: Principal Investigator
    Theory of Biomolecular Diffusion
    NIH/NIGMS R01GM031479Jun 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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Predicting the effects of dATP on cardiac contraction using multiscale modeling of the sarcomere. Arch Biochem Biophys. 2020 Sep 18; 108582. McCabe KJ, Aboelkassem Y, Teitgen AE, Huber GA, McCammon JA, Regnier M, McCulloch AD. PMID: 32956632.
      View in: PubMed   Mentions:    Fields:    
    2. 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:    Fields:    
    3. 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:
    4. 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: 2     Fields:    Translation:Cells
    5. 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: 1     Fields:    Translation:HumansCells
    6. 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:    Fields:    
    7. Brownian Dynamics Simulations of Biological Molecules. Trends Chem. 2019 Nov; 1(8):727-738. Huber GA, McCammon JA. PMID: 32309795.
      View in: PubMed   Mentions:
    8. 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:    Fields:    Translation:Cells
    9. 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
    10. 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:
    11. 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 07 23; 116(30):14989-14994. Zhou S, Weiß RG, Cheng LT, Dzubiella J, McCammon JA, Li B. PMID: 31270236.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    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:    Fields:    Translation:Cells
    13. The invisible dance of CRISPR-Cas9. Simulations unveil the molecular side of the gene-editing revolution. Phys Today. 2019 Apr; 72(4):30-36. Palermo G, Ricci CG, McCammon JA. PMID: 31511751.
      View in: PubMed   Mentions:
    14. 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
    15. 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:
    16. 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:    Fields:    Translation:Cells
    17. 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: 27     Fields:    Translation:HumansAnimalsCells
    18. 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: 1     Fields:    Translation:Cells
    19. 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: 1     Fields:    Translation:Cells
    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: 6     Fields:    Translation:AnimalsCells
    21. 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: 1     Fields:    Translation:HumansCells
    22. A Computational Modeling Approach Predicts Interaction of the Antifungal Protein AFP from Aspergillus giganteus with Fungal Membranes via Its γ-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: 6     Fields:    Translation:AnimalsCells
    23. 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: 1     Fields:    Translation:HumansCells
    24. 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: 7     Fields:    Translation:HumansCells
    25. HIERARCHICAL ORTHOGONAL MATRIX GENERATION AND MATRIX-VECTOR MULTIPLICATIONS IN RIGID BODY SIMULATIONS. SIAM J Sci Comput. 2018; 40(3):A1345-A1361. Fang F, Huang J, Huber G, McCammon JA, Zhang BO. PMID: 31452593.
      View in: PubMed   Mentions:
    26. 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: 19     Fields:    Translation:Cells
    27. 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: 4     Fields:    Translation:Cells
    28. 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: 2     Fields:    Translation:Cells
    29. 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: 17     Fields:    Translation:Cells
    30. 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: 9     Fields:    Translation:HumansCells
    31. 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:
    32. 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: 2     Fields:    Translation:Cells
    33. 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:
    34. 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:    Fields:    Translation:AnimalsCells
    35. 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
    36. 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: 106     Fields:    
    37. 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: 2     Fields:    Translation:Cells
    38. Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications. Annu Rep Comput Chem. 2017; 13:231-278. Miao Y, McCammon JA. PMID: 29720925.
      View in: PubMed   Mentions:
    39. 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: 15     Fields:    Translation:Cells
    40. 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: 5     Fields:    Translation:HumansCells
    41. "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
    42. 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: 18     Fields:    Translation:Cells
    43. 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: 2     Fields:    Translation:HumansCells
    44. 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
    45. 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
    46. 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: 1     Fields:    Translation:HumansCells
    47. 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: 21     Fields:    Translation:Cells
    48. 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: 22     Fields:    Translation:HumansCells
    49. 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:
    50. 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: 18     Fields:    Translation:HumansAnimalsCells
    51. 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:    Fields:    Translation:AnimalsCells
    52. 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:    
    53. 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:    
    54. 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:
    55. 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: 25     Fields:    Translation:HumansCells
    56. 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: 4     Fields:    Translation:Cells
    57. 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
    58. 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:    
    59. 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: 10     Fields:    Translation:Cells
    60. 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
    61. Computation of pH-dependent binding free energies. Biopolymers. 2016 Jan; 105(1):43-9. Kim MO, McCammon JA. PMID: 26202905.
      View in: PubMed   Mentions: 4     Fields:    
    62. 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
    63. 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: 37     Fields:    Translation:HumansCells
    64. 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: 32     Fields:    Translation:HumansCells
    65. 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: 7     Fields:    Translation:Cells
    66. 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: 16     Fields:    Translation:HumansAnimalsCells
    67. 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
    68. 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
    69. 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: 68     Fields:    
    70. 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: 7     Fields:    Translation:HumansCells
    71. 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
    72. 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: 18     Fields:    Translation:Cells
    73. 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: 12     Fields:    Translation:Cells
    74. 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: 4     Fields:    Translation:HumansCells
    75. 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: 7     Fields:    Translation:HumansCells
    76. 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: 29     Fields:    Translation:Cells
    77. 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.
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    78. 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.
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    79. 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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    80. 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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    81. 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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    82. 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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    83. 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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    84. 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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    85. 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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    86. 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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    87. 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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    88. 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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    89. 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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    90. 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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    91. 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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    92. 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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    93. 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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    94. 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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    95. 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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    96. 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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    97. 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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    98. 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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    99. 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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    100. 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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    101. 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. Kekenes-Huskey PM, Gillette AK, McCammon JA. PMID: 24811624.
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    102. 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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    103. 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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    104. '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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    105. 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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    106. 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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    107. 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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    108. 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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    109. 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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    110. 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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    111. 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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    112. 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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    113. 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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    114. 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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    115. 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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    116. 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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    117. 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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    118. 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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    119. 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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    120. 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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    121. 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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    122. 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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    123. 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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    124. Simulations of biased agonists in the ß(2) adrenergic receptor with accelerated molecular dynamics. Biochemistry. 2013 Aug 20; 52(33):5593-603. Tikhonova IG, Selvam B, Ivetac A, Wereszczynski J, McCammon JA. PMID: 23879802.
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    125. 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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    126. 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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    127. 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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    128. 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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    129. 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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    130. 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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    131. 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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    132. 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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    133. 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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    134. 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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    135. 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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    136. 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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    137. 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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    138. 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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    139. 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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    140. Molecular recognition and ligand association. Annu Rev Phys Chem. 2013; 64:151-75. Baron R, McCammon JA. PMID: 23473376.
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    141. 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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    142. 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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    143. 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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    144. 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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    145. 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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    146. 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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    147. 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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    148. 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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    149. 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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    150. 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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    151. 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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    152. 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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    153. 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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    154. 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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    155. 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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    156. 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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    157. 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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    158. 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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    159. 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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    160. 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.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    161. 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.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    162. 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.
      View in: PubMed   Mentions:    Fields:    
    163. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    164. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    165. 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: 9     Fields:    Translation:Cells
    166. 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
    167. 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: 24     Fields:    Translation:Cells
    168. 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
    169. 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: 42     Fields:    Translation:AnimalsCells
    170. AutoClickChem: click chemistry in silico. PLoS Comput Biol. 2012; 8(3):e1002397. Durrant JD, McCammon JA. PMID: 22438795.
      View in: PubMed   Mentions: 10     Fields:    
    171. 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
    172. 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: 22     Fields:    Translation:Cells
    173. 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
    174. 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: 23     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: 9     Fields:    Translation:HumansCells
    176. 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
    177. 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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    178. 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: 2     Fields:    Translation:Cells
    179. 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
    180. 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
    181. 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.
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    182. 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: 23     Fields:    Translation:Cells
    183. 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:    
    184. 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: 34     Fields:    Translation:Cells
    185. 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. Bucher D, Grant BJ, McCammon JA. PMID: 22050600.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    186. NNScore 2.0: a neural-network receptor-ligand scoring function. J Chem Inf Model. 2011 Nov 28; 51(11):2897-903. Durrant JD, McCammon JA. PMID: 22017367.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansCells
    187. Molecular dynamics simulations and drug discovery. BMC Biol. 2011 Oct 28; 9:71. Durrant JD, McCammon JA. PMID: 22035460.
      View in: PubMed   Mentions: 132     Fields:    Translation:HumansCells
    188. Novel allosteric sites on Ras for lead generation. PLoS One. 2011; 6(10):e25711. Grant BJ, Lukman S, Hocker HJ, Sayyah J, Brown JH, McCammon JA, Gorfe AA. PMID: 22046245.
      View in: PubMed   Mentions: 46     Fields:    Translation:HumansCells
    189. Studying functional dynamics in bio-molecules using accelerated molecular dynamics. Phys Chem Chem Phys. 2011 Dec 07; 13(45):20053-65. Markwick PR, McCammon JA. PMID: 22015376.
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    190. Large-scale conformational changes of Trypanosoma cruzi proline racemase predicted by accelerated molecular dynamics simulation. PLoS Comput Biol. 2011 Oct; 7(10):e1002178. de Oliveira CA, Grant BJ, Zhou M, McCammon JA. PMID: 22022240.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    191. CrystalDock: a novel approach to fragment-based drug design. J Chem Inf Model. 2011 Oct 24; 51(10):2573-80. Durrant JD, Friedman AJ, McCammon JA. PMID: 21910501.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    192. Towards the development of novel Trypanosoma brucei RNA editing ligase 1 inhibitors. BMC Pharmacol. 2011 Aug 30; 11:9. Durrant JD, McCammon JA. PMID: 21878090.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    193. Measuring the successes and deficiencies of constant pH molecular dynamics: a blind prediction study. Proteins. 2011 Dec; 79(12):3381-8. Williams SL, Blachly PG, McCammon JA. PMID: 22072520.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    194. Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics. J Chem Theory Comput. 2011 Oct 11; 7(10):3199-3207. Wang Y, Markwick PR, de Oliveira CA, McCammon JA. PMID: 22003320.
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    195. HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis. J Mol Graph Model. 2011 Nov; 31:5-9. Durrant JD, McCammon JA. PMID: 21880522.
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    196. Non-bisphosphonate inhibitors of isoprenoid biosynthesis identified via computer-aided drug design. Chem Biol Drug Des. 2011 Sep; 78(3):323-32. Durrant JD, Cao R, Gorfe AA, Zhu W, Li J, Sankovsky A, Oldfield E, McCammon JA. PMID: 21696546.
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    197. 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. Romanowska J, McCammon JA, Trylska J. PMID: 21814503.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    198. 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. Durrant JD, de Oliveira CA, McCammon JA. PMID: 21609408.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    199. Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies. J Chem Theory Comput. 2011 Jun 02; 7(7):2224-2232. Lawrenz M, Baron R, Wang Y, McCammon JA. PMID: 21811708.
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    200. Predictive power of molecular dynamics receptor structures in virtual screening. J Chem Inf Model. 2011 Jun 27; 51(6):1439-46. Nichols SE, Baron R, Ivetac A, McCammon JA. PMID: 21534609.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    201. Accelerating chemical reactions: exploring reactive free-energy surfaces using accelerated ab initio molecular dynamics. J Chem Phys. 2011 May 07; 134(17):174107. Pierce LC, Markwick PR, McCammon JA, Doltsinis NL. PMID: 21548673.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    202. Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics. PLoS Comput Biol. 2011 Apr; 7(4):e1002034. Bucher D, Grant BJ, Markwick PR, McCammon JA. PMID: 21533070.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
    203. 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. Sinko W, de Oliveira C, Williams S, Van Wynsberghe A, Durrant JD, Cao R, Oldfield E, McCammon JA. PMID: 21294851.
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    204. Brownian dynamics study of the association between the 70S ribosome and elongation factor G. Biopolymers. 2011 Sep; 95(9):616-27. Dlugosz M, Huber GA, McCammon JA, Trylska J. PMID: 21394717.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    205. Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations. PLoS Comput Biol. 2011 Mar; 7(3):e1002004. Skjaerven L, Grant B, Muga A, Teigen K, McCammon JA, Reuter N, Martinez A. PMID: 21423709.
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    206. 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. Bucher D, Pierce LC, McCammon JA, Markwick PR. PMID: 21494425.
      View in: PubMed   Mentions: 10     Fields:    
    207. Diffusion and association processes in biological systems: theory, computation and experiment. BMC Biophys. 2011 Mar 02; 4:2. Mereghetti P, Kokh D, McCammon JA, Wade RC. PMID: 21595997.
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    208. Gated Diffusion-controlled Reactions. BMC Biophys. 2011 Mar 02; 4:4. McCammon JA. PMID: 21595999.
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    209. 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
    210. Molecular mimicry and ligand recognition in binding and catalysis by the histone demethylase LSD1-CoREST complex. Structure. 2011 Feb 09; 19(2):212-20. Baron R, Binda C, Tortorici M, McCammon JA, Mattevi A. PMID: 21300290.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansAnimalsCells
    211. 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. Williams SL, de Oliveira CA, Vazquez H, McCammon JA. PMID: 21266015.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    212. BINANA: a novel algorithm for ligand-binding characterization. J Mol Graph Model. 2011 Apr; 29(6):888-93. Durrant JD, McCammon JA. PMID: 21310640.
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    213. Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam. J Phys Chem Lett. 2011 Feb 03; 2(3):158-164. Markwick PR, Pierce LC, Goodin DB, McCammon JA. PMID: 21307966.
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    214. Molecular recognition in the case of flexible targets. Curr Pharm Des. 2011; 17(17):1663-71. Ivetac A, McCammon JA. PMID: 21619526.
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    215. Implementation of Accelerated Molecular Dynamics in NAMD. Comput Sci Discov. 2011; 4(1). Wang Y, Harrison CB, Schulten K, McCammon JA. PMID: 21686063.
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    216. Conformational selection in G-proteins: lessons from Ras and Rho. Biophys J. 2010 Dec 01; 99(11):L87-9. Grant BJ, McCammon JA, Gorfe AA. PMID: 21112273.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    217. POVME: an algorithm for measuring binding-pocket volumes. J Mol Graph Model. 2011 Feb; 29(5):773-6. Durrant JD, de Oliveira CA, McCammon JA. PMID: 21147010.
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    218. Browndye: A Software Package for Brownian Dynamics. Comput Phys Commun. 2010 Nov 01; 181(11):1896-1905. Huber GA, McCammon JA. PMID: 21132109.
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    219. Characterization of a clinical polymer-drug conjugate using multiscale modeling. Biopolymers. 2010 Nov; 93(11):936-51. Peng LX, Ivetac A, Chaudhari AS, Van S, Zhao G, Yu L, Howell SB, McCammon JA, Gough DA. PMID: 20564048.
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    220. 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. Cheng Y, Yu Z, Hoshijima M, Holst MJ, McCulloch AD, McCammon JA, Michailova AP. PMID: 21060856.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCells
    221. 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. Durrant JD, McCammon JA. PMID: 20845954.
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    222. 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. Sierecki E, Sinko W, McCammon JA, Newton AC. PMID: 20836557.
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    223. Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations. J Chem Theory Comput. 2010 Nov 09; 6(11):3285-3292. Wereszczynski J, McCammon JA. PMID: 21072329.
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    224. Computer-aided drug-discovery techniques that account for receptor flexibility. Curr Opin Pharmacol. 2010 Dec; 10(6):770-4. Durrant JD, McCammon JA. PMID: 20888294.
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    225. Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions. J Comput Phys. 2010 Sep 20; 229(19):6979-6994. Lu B, Holst MJ, McCammon JA, Zhou YC. PMID: 21709855.
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    226. The distinct conformational dynamics of K-Ras and H-Ras A59G. PLoS Comput Biol. 2010 Sep 09; 6(9). Lukman S, Grant BJ, Gorfe AA, Grant GH, McCammon JA. PMID: 20838576.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansCells
    227. Water in cavity-ligand recognition. J Am Chem Soc. 2010 Sep 01; 132(34):12091-7. Baron R, Setny P, McCammon JA. PMID: 20695475.
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    228. Porous protein frameworks with unsaturated metal centers in sterically encumbered coordination sites. Chem Commun (Camb). 2011 Jan 07; 47(1):313-5. Radford RJ, Lawrenz M, Nguyen PC, McCammon JA, Tezcan FA. PMID: 20740227.
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    229. How Can Hydrophobic Association Be Enthalpy Driven? J Chem Theory Comput. 2010 Sep 14; 6(9):2866-2871. Setny P, Baron R, McCammon JA. PMID: 20844599.
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    230. Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy. Proteins. 2010 Aug 15; 78(11):2523-32. Lawrenz M, Wereszczynski J, Amaro R, Walker R, Roitberg A, McCammon JA. PMID: 20602360.
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    231. Solvation Effect on the Conformations of Alanine Dipeptide: Integral Equation Approach. J Phys Chem Lett. 2010 Aug 05; 1(15):2279-2283. Ishizuka R, Huber GA, McCammon JA. PMID: 20694049.
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    232. 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. Durrant JD, Urbaniak MD, Ferguson MA, McCammon JA. PMID: 20527952.
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    233. 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. Ivetac A, McCammon JA. PMID: 20626410.
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    234. From sensors to silencers: quinoline- and benzimidazole-sulfonamides as inhibitors for zinc proteases. J Am Chem Soc. 2010 Jun 23; 132(24):8232-3. Rouffet M, de Oliveira CA, Udi Y, Agrawal A, Sagi I, McCammon JA, Cohen SM. PMID: 20507095.
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    235. 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. Tainer JA, McCammon JA, Ivanov I. PMID: 20455582.
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    236. AFMPB: An Adaptive Fast Multipole Poisson-Boltzmann Solver for Calculating Electrostatics in Biomolecular Systems. Comput Phys Commun. 2010 Jun 01; 181(6):1150-1160. Lu B, Cheng X, Huang J, McCammon JA. PMID: 20532187.
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    237. Computational identification of uncharacterized cruzain binding sites. PLoS Negl Trop Dis. 2010 May 11; 4(5):e676. Durrant JD, Keränen H, Wilson BA, McCammon JA. PMID: 20485483.
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    238. Channeling by Proximity: The Catalytic Advantages of Active Site Colocalization Using Brownian Dynamics. J Phys Chem Lett. 2010 May 06; 1(9):1332-1335. Bauler P, Huber G, Leyh T, McCammon JA. PMID: 20454551.
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    239. Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug design. Comput Biol Chem. 2010 Apr; 34(2):97-105. Durrant JD, McCammon JA. PMID: 20427241.
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    240. Solutions to a reduced Poisson-Nernst-Planck system and determination of reaction rates. Physica A. 2010 Apr 01; 389(7):1329-1345. Li B, Lu B, Wang Z, McCammon JA. PMID: 20228879.
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    241. Role of secondary sialic acid binding sites in influenza N1 neuraminidase. J Am Chem Soc. 2010 Mar 10; 132(9):2883-5. Sung JC, Van Wynsberghe AW, Amaro RE, Li WW, McCammon JA. PMID: 20155919.
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    242. Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitors. J Mol Recognit. 2010 Mar-Apr; 23(2):173-82. Durrant JD, de Oliveira CA, McCammon JA. PMID: 19882751.
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    243. Enhanced conformational space sampling improves the prediction of chemical shifts in proteins. J Am Chem Soc. 2010 Feb 03; 132(4):1220-1. Markwick PR, Cervantes CF, Abel BL, Komives EA, Blackledge M, McCammon JA. PMID: 20063881.
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    244. A dynamic model of HIV integrase inhibition and drug resistance. J Mol Biol. 2010 Mar 26; 397(2):600-15. Perryman AL, Forli S, Morris GM, Burt C, Cheng Y, Palmer MJ, Whitby K, McCammon JA, Phillips C, Olson AJ. PMID: 20096702.
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    245. A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. PLoS Comput Biol. 2010 Jan 22; 6(1):e1000648. Durrant JD, Amaro RE, Xie L, Urbaniak MD, Ferguson MA, Haapalainen A, Chen Z, Di Guilmi AM, Wunder F, Bourne PE, McCammon JA. PMID: 20098496.
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    246. Kinetics of diffusion-controlled enzymatic reactions with charged substrates. PMC Biophys. 2010 Jan 18; 3:1. Lu B, McCammon JA. PMID: 20157429.
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    247. Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics. J Chem Theory Comput. 2010 Feb 09; 6(2):560-568. Williams SL, de Oliveira CA, McCammon JA. PMID: 20148176.
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    248. Large conformational changes in proteins: signaling and other functions. Curr Opin Struct Biol. 2010 Apr; 20(2):142-7. Grant BJ, Gorfe AA, McCammon JA. PMID: 20060708.
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    249. 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. Baron R, Hünenberger PH, McCammon JA. PMID: 20011626.
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    250. 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. Khavrutskii IV, Grant B, Taylor SS, McCammon JA. PMID: 19886670.
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    251. 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. Newhouse EI, Xu D, Markwick PR, Amaro RE, Pao HC, Wu KJ, Alam M, McCammon JA, Li WW. PMID: 19891427.
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    252. Toward a unified representation of protein structural dynamics in solution. J Am Chem Soc. 2009 Nov 25; 131(46):16968-75. Markwick PR, Bouvignies G, Salmon L, McCammon JA, Nilges M, Blackledge M. PMID: 19919148.
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    253. 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. Sivendran S, Jones V, Sun D, Wang Y, Grzegorzewicz AE, Scherman MS, Napper AD, McCammon JA, Lee RE, Diamond SL, McNeil M. PMID: 19969466.
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    254. The gates of ion channels and enzymes. Trends Biochem Sci. 2010 Mar; 35(3):179-85. Zhou HX, McCammon JA. PMID: 19926290.
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    255. The oxygen-binding vs. oxygen-consuming paradigm in biocatalysis: structural biology and biomolecular simulation. Curr Opin Struct Biol. 2009 Dec; 19(6):672-9. Baron R, McCammon JA, Mattevi A. PMID: 19896366.
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    256. Dewetting-controlled binding of ligands to hydrophobic pockets. Phys Rev Lett. 2009 Oct 30; 103(18):187801. Setny P, Wang Z, Cheng LT, Li B, McCammon JA, Dzubiella J. PMID: 19905832.
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    257. Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach. J Chem Phys. 2009 Oct 14; 131(14):144102. Cheng LT, Wang Z, Setny P, Dzubiella J, Li B, McCammon JA. PMID: 19831428.
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    258. 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. Cervantes CF, Markwick PR, Sue SC, McCammon JA, Dyson HJ, Komives EA. PMID: 19591507.
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    259. The role of conserved water molecules in the catalytic domain of protein kinases. Proteins. 2009 Aug 15; 76(3):527-35. Knight JD, Hamelberg D, McCammon JA, Kothary R. PMID: 19425109.
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    260. Enzymatic activity versus structural dynamics: the case of acetylcholinesterase tetramer. Biophys J. 2009 Aug 05; 97(3):897-905. Gorfe AA, Lu B, Yu Z, McCammon JA. PMID: 19651048.
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    261. Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics. J Comput Chem. 2009 Aug; 30(11):1719-25. Fajer M, Swift RV, McCammon JA. PMID: 19421994.
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    262. 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. Burke JE, Babakhani A, Gorfe AA, Kokotos G, Li S, Woods VL, McCammon JA, Dennis EA. PMID: 19459633.
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    263. Multiple pathways guide oxygen diffusion into flavoenzyme active sites. Proc Natl Acad Sci U S A. 2009 Jun 30; 106(26):10603-8. 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. PMID: 19541622.
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    264. Molecular-dynamics simulations of ELIC-a prokaryotic homologue of the nicotinic acetylcholine receptor. Biophys J. 2009 Jun 03; 96(11):4502-13. Cheng X, Ivanov I, Wang H, Sine SM, McCammon JA. PMID: 19486673.
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    265. An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics. J Chem Theory Comput. 2009 Jun 09; 5(6):1692-1699. Lu B, Cheng X, Huang J, McCammon JA. PMID: 19517026.
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    266. Single-channel current through nicotinic receptor produced by closure of binding site C-loop. Biophys J. 2009 May 06; 96(9):3582-90. Wang HL, Toghraee R, Papke D, Cheng XL, McCammon JA, Ravaioli U, Sine SM. PMID: 19413963.
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    267. 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.
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    268. 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. Swift RV, McCammon JA. PMID: 19301911.
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    269. 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. Amaro RE, Cheng X, Ivanov I, Xu D, McCammon JA. PMID: 19296611.
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    270. 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. Lawrenz M, Baron R, McCammon JA. PMID: 19461872.
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    271. 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. Ivetac A, McCammon JA. PMID: 19324058.
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    272. Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. PLoS Comput Biol. 2009 Mar; 5(3):e1000325. Grant BJ, Gorfe AA, McCammon JA. PMID: 19300489.
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    273. Multiscale modeling in rodent ventricular myocytes. IEEE Eng Med Biol Mag. 2009 Mar-Apr; 28(2):46-57. 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. PMID: 19349251.
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    274. Thioamide hydroxypyrothiones supersede amide hydroxypyrothiones in potency against anthrax lethal factor. J Med Chem. 2009 Feb 26; 52(4):1063-74. Agrawal A, de Oliveira CA, Cheng Y, Jacobsen JA, McCammon JA, Cohen SM. PMID: 19170530.
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    275. 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. Khavrutskii IV, Gorfe AA, Lu B, McCammon JA. PMID: 19146415.
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    276. 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. Cheng LT, Xie Y, Dzubiella J, McCammon JA, Che J, Li B. PMID: 20150952.
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    277. 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. Xu D, Newhouse EI, Amaro RE, Pao HC, Cheng LS, Markwick PR, McCammon JA, Li WW, Arzberger PW. PMID: 19356594.
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    278. Toward understanding the conformational dynamics of RNA ligation. Biochemistry. 2009 Feb 03; 48(4):709-19. Swift RV, Durrant J, Amaro RE, McCammon JA. PMID: 19133737.
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    279. AutoGrow: a novel algorithm for protein inhibitor design. Chem Biol Drug Des. 2009 Feb; 73(2):168-78. Durrant JD, Amaro RE, McCammon JA. PMID: 19207419.
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    280. 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. Wong S, Amaro RE, McCammon JA. PMID: 19461869.
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    281. Mechanistic insight into the role of transition-state stabilization in cyclophilin A. J Am Chem Soc. 2009 Jan 14; 131(1):147-52. Hamelberg D, McCammon JA. PMID: 19128175.
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    282. A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach. Comput Biol Chem. 2009 Apr; 33(2):160-70. Babakhani A, Talley TT, Taylor P, McCammon JA. PMID: 19186108.
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    283. Finite element analysis of drug electrostatic diffusion: inhibition rate studies in N1 neuraminidase. Pac Symp Biocomput. 2009; 281-92. Cheng Y, Holst MJ, McCammon JA. PMID: 19209708.
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    284. 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. Baron R, Wong SE, de Oliveira CA, McCammon JA. PMID: 19053689.
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    285. 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. Amaro RE, Schnaufer A, Interthal H, Hol W, Stuart KD, McCammon JA. PMID: 18981420.
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    286. Hot-spot residues at the E9/Im9 interface help binding via different mechanisms. Biopolymers. 2008 Nov; 89(11):916-20. Wong SE, Baron R, McCammon JA. PMID: 18546205.
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    287. 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. Yu Z, Holst MJ, Hayashi T, Bajaj CL, Ellisman MH, McCammon JA, Hoshijima M. PMID: 18835449.
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    288. 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. Khavrutskii IV, Fajer M, McCammon JA. PMID: 20357907.
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    289. Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration. J Chem Theory Comput. 2008 Oct 14; 4(10):1565-1569. Fajer M, Hamelberg D, McCammon JA. PMID: 19461870.
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    290. 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. Gorfe AA, McCammon JA. PMID: 18761454.
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    291. Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations. J Chem Theory Comput. 2008 Sep 09; 4(9):1516-1525. de Oliveira CA, Hamelberg D, McCammon JA. PMID: 19461868.
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    292. 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. Cheng Y, Chang CE, Yu Z, Zhang Y, Sun M, Leyh TS, Holst MJ, McCammon JA. PMID: 18689458.
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    293. Thermodynamics of peptide insertion and aggregation in a lipid bilayer. J Phys Chem B. 2008 Aug 28; 112(34):10528-34. Babakhani A, Gorfe AA, Kim JE, McCammon JA. PMID: 18681475.
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    294. 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. Mura C, McCammon JA. PMID: 18653524.
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    295. Water-membrane partition thermodynamics of an amphiphilic lipopeptide: an enthalpy-driven hydrophobic effect. Biophys J. 2008 Oct; 95(7):3269-77. Gorfe AA, Baron R, McCammon JA. PMID: 18621822.
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    296. Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem. 2008 Jul 10; 51(13):3878-94. Cheng LS, Amaro RE, Xu D, Li WW, Arzberger PW, McCammon JA. PMID: 18558668.
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    297. Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins. Structure. 2008 Jun; 16(6):885-96. Gorfe AA, Grant BJ, McCammon JA. PMID: 18547521.
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    298. 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. Chang CE, McLaughlin WA, Baron R, Wang W, McCammon JA. PMID: 18495919.
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    299. (Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding. Chemphyschem. 2008 May 16; 9(7):983-8. Baron R, McCammon JA. PMID: 18418822.
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    300. Acetylcholinesterase: mechanisms of covalent inhibition of H447I mutant determined by computational analyses. Chem Biol Interact. 2008 Sep 25; 175(1-3):196-9. Cheng YH, Cheng XL, Radic Z, McCammon JA. PMID: 18657802.
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    301. Inhibition of cathepsin B by Au(I) complexes: a kinetic and computational study. J Biol Inorg Chem. 2008 May; 13(4):555-61. Gunatilleke SS, de Oliveira CA, McCammon JA, Barrios AM. PMID: 18253767.
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    302. A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces. J Math Anal Appl. 2008 Apr 01; 340(1):135-164. Zhou YC, Holst M, McCammon JA. PMID: 19461946.
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    303. Catalytically requisite conformational dynamics in the mRNA-capping enzyme probed by targeted molecular dynamics. Biochemistry. 2008 Apr 01; 47(13):4102-11. Swift RV, McCammon JA. PMID: 18330997.
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    304. Electrostatic free energy and its variations in implicit solvent models. J Phys Chem B. 2008 Mar 13; 112(10):3058-69. Che J, Dzubiella J, Li B, McCammon JA. PMID: 18275182.
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    305. A novel switch region regulates H-ras membrane orientation and signal output. EMBO J. 2008 Mar 05; 27(5):727-35. Abankwa D, Hanzal-Bayer M, Ariotti N, Plowman SJ, Gorfe AA, Parton RG, McCammon JA, Hancock JF. PMID: 18273062.
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    306. Feature-preserving adaptive mesh generation for molecular shape modeling and simulation. J Mol Graph Model. 2008 Jun; 26(8):1370-80. Yu Z, Holst MJ, Cheng Y, McCammon JA. PMID: 18337134.
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    307. Control of cation permeation through the nicotinic receptor channel. PLoS Comput Biol. 2008 Feb; 4(2):e41. Wang HL, Cheng X, Taylor P, McCammon JA, Sine SM. PMID: 18282090.
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    308. 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. Khavrutskii IV, Dzubiella J, McCammon JA. PMID: 18247929.
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    309. Molecular surface-free continuum model for electrodiffusion processes. Chem Phys Lett. 2008 Jan 21; 451(4-6):282-286. Lu B, McCammon JA. PMID: 19461944.
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    310. 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. Landon MR, Amaro RE, Baron R, Ngan CH, Ozonoff D, McCammon JA, Vajda S. PMID: 18205727.
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    311. An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des. 2008 Sep; 22(9):693-705. Amaro RE, Baron R, McCammon JA. PMID: 18196463.
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    312. Springs and speeds in free energy reconstruction from irreversible single-molecule pulling experiments. J Phys Chem B. 2008 May 15; 112(19):5892-7. Minh DD, McCammon JA. PMID: 18088108.
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    313. Continuum simulations of acetylcholine consumption by acetylcholinesterase: a Poisson-Nernst-Planck approach. J Phys Chem B. 2008 Jan 17; 112(2):270-5. Zhou YC, Lu B, Huber GA, Holst MJ, McCammon JA. PMID: 18052268.
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    314. 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. Amaro RE, Swift RV, McCammon JA. PMID: 18060084.
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    315. 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. de Oliveira CA, Hamelberg D, McCammon JA. PMID: 17994855.
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    316. Accelerated entropy estimates with accelerated dynamics. J Chem Phys. 2007 Oct 21; 127(15):154105. Minh DD, Hamelberg D, McCammon JA. PMID: 17949130.
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    317. 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. Cerutti DS, Baker NA, McCammon JA. PMID: 17949217.
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    318. Sampling of slow diffusive conformational transitions with accelerated molecular dynamics. J Chem Phys. 2007 Oct 21; 127(15):155102. Hamelberg D, de Oliveira CA, McCammon JA. PMID: 17949218.
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    319. Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution. J Chem Phys. 2007 Oct 07; 127(13):135102. Lu B, Zhou YC, Huber GA, Bond SD, Holst MJ, McCammon JA. PMID: 17919055.
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    320. Dynamics of the acetylcholinesterase tetramer. Biophys J. 2008 Feb 15; 94(4):1144-54. Gorfe AA, Chang CE, Ivanov I, McCammon JA. PMID: 17921202.
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    321. "New-version-fast-multipole-method" accelerated electrostatic interactions in biomolecular systems. J Comput Phys. 2007 Oct 01; 226(2):1348-1366. Lu B, Cheng X, McCammon JA. PMID: 18379638.
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    322. 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. Khavrutskii IV, McCammon JA. PMID: 17902931.
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    323. H-ras protein in a bilayer: interaction and structure perturbation. J Am Chem Soc. 2007 Oct 10; 129(40):12280-6. Gorfe AA, Babakhani A, McCammon JA. PMID: 17880077.
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    324. 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. Hamelberg D, Shen T, McCammon JA. PMID: 17823247.
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    325. Application of the level-set method to the implicit solvation of nonpolar molecules. J Chem Phys. 2007 Aug 28; 127(8):084503. Cheng LT, Dzubiella J, McCammon JA, Li B. PMID: 17764265.
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    326. 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. Baron R, McCammon JA. PMID: 17718514.
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    327. Nanosecond-timescale conformational dynamics of the human alpha7 nicotinic acetylcholine receptor. Biophys J. 2007 Oct 15; 93(8):2622-34. Cheng X, Ivanov I, Wang H, Sine SM, McCammon JA. PMID: 17573436.
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    328. 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. Ivanov I, Cheng X, Sine SM, McCammon JA. PMID: 17552523.
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    329. 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. Amaro RE, Minh DD, Cheng LS, Lindstrom WM, Olson AJ, Lin JH, Li WW, McCammon JA. PMID: 17539643.
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    330. Improved Boundary Element Methods for Poisson-Boltzmann Electrostatic Potential and Force Calculations. J Chem Theory Comput. 2007 May; 3(3):1134-42. Lu B, McCammon JA. PMID: 26627432.
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    331. Comparative MD analysis of the stability of transthyretin providing insight into the fibrillation mechanism. Biopolymers. 2007 May; 86(1):73-82. Sørensen J, Hamelberg D, Schiøtt B, McCammon JA. PMID: 17315201.
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    332. 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. Cheng Y, Cheng X, Radic Z, McCammon JA. PMID: 17461584.
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    333. 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. Grant BJ, McCammon JA, Caves LS, Cross RA. PMID: 17399740.
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    334. HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics. Biophys J. 2007 Jun 15; 92(12):4179-87. Trylska J, Tozzini V, Chang CE, McCammon JA. PMID: 17384072.
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    335. Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophys J. 2007 May 15; 92(10):3397-406. Cheng Y, Suen JK, Zhang D, Bond SD, Zhang Y, Song Y, Baker NA, Bajaj CL, Holst MJ, McCammon JA. PMID: 17307827.
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    336. 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. Gorfe AA, Hanzal-Bayer M, Abankwa D, Hancock JF, McCammon JA. PMID: 17263520.
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    337. 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. Ivanov I, Tainer JA, McCammon JA. PMID: 17242363.
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    338. Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction models. Biophys Chem. 2007 May; 127(3):129-39. Cheng Y, Suen JK, Radic Z, Bond SD, Holst MJ, McCammon JA. PMID: 17307283.
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    339. SR protein kinase 1 is resilient to inactivation. Structure. 2007 Jan; 15(1):123-33. Ngo JC, Gullingsrud J, Giang K, Yeh MJ, Fu XD, Adams JA, McCammon JA, Ghosh G. PMID: 17223538.
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    340. Generalized Born model with a simple, robust molecular volume correction. J Chem Theory Comput. 2007 Jan 01; 3(1):156-169. Mongan J, Simmerling C, McCammon JA, Case DA, Onufriev A. PMID: 21072141.
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    341. Binding pathways of ligands to HIV-1 protease: coarse-grained and atomistic simulations. Chem Biol Drug Des. 2007 Jan; 69(1):5-13. Chang CE, Trylska J, Tozzini V, McCammon JA. PMID: 17313452.
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    342. Free energy profile of H-ras membrane anchor upon membrane insertion. Angew Chem Int Ed Engl. 2007; 46(43):8234-7. Gorfe AA, Babakhani A, McCammon JA. PMID: 17886310.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    343. 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. de Oliveira CA, Zissen M, Mongon J, McCammon JA. PMID: 18220784.
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    344. Towards an in vivo biologically inspired nanofactory. Nat Nanotechnol. 2007 Jan; 2(1):3-7. 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. PMID: 18654192.
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    345. 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. Swanson JM, Wagoner JA, Baker NA, McCammon JA. PMID: 26627162.
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    346. 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. Lu B, Cheng X, Huang J, McCammon JA. PMID: 17148613.
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    347. On the application of accelerated molecular dynamics to liquid water simulations. J Phys Chem B. 2006 Nov 16; 110(45):22695-701. de Oliveira CA, Hamelberg D, McCammon JA. PMID: 17092018.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    348. Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications. Nucleic Acids Res. 2006; 34(20):6023-33. Ivanov I, Chapados BR, McCammon JA, Tainer JA. PMID: 17071716.
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    349. 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. Senapati S, Cheng Y, McCammon JA. PMID: 17034128.
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    350. 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. Bui JM, McCammon JA. PMID: 17021015.
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    351. 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. Yang G, Trylska J, Tor Y, McCammon JA. PMID: 16942021.
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    352. Insight into the role of hydration on protein dynamics. J Chem Phys. 2006 Sep 07; 125(9):094905. Hamelberg D, Shen T, McCammon JA. PMID: 16965117.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    353. Configurational-bias sampling technique for predicting side-chain conformations in proteins. Protein Sci. 2006 Sep; 15(9):2029-39. Jain T, Cerutti DS, McCammon JA. PMID: 16943441.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    354. Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics. 2006 Nov 01; 22(21):2695-6. Grant BJ, Rodrigues AP, ElSawy KM, McCammon JA, Caves LS. PMID: 16940322.
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    355. Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors. PLoS Comput Biol. 2006 Sep 29; 2(9):e134. Cheng X, Wang H, Grant B, Sine SM, McCammon JA. PMID: 17009865.
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    356. Flap opening dynamics in HIV-1 protease explored with a coarse-grained model. J Struct Biol. 2007 Mar; 157(3):606-15. Tozzini V, Trylska J, Chang CE, McCammon JA. PMID: 17029846.
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    357. CIRSE: a solvation energy estimator compatible with flexible protein docking and design applications. Protein Sci. 2006 Jul; 15(7):1579-96. Cerutti DS, Jain T, McCammon JA. PMID: 16815913.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    358. Evaluation and binding-mode prediction of thiopyrone-based inhibitors of anthrax lethal factor. ChemMedChem. 2006 Jul; 1(7):694-7. Lewis JA, Mongan J, McCammon JA, Cohen SM. PMID: 16902919.
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    359. 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. Perryman AL, Lin JH, McCammon JA. PMID: 16508951.
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    360. Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers. 2006 Jun 05; 82(2):106-20. Konecny R, Trylska J, Tama F, Zhang D, Baker NA, Brooks CL, McCammon JA. PMID: 16278831.
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    361. The influence of macromolecular crowding on HIV-1 protease internal dynamics. J Am Chem Soc. 2006 May 10; 128(18):6006-7. Minh DD, Chang CE, Trylska J, Tozzini V, McCammon JA. PMID: 16669648.
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    362. Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev. 2006 May; 106(5):1589-615. Adcock SA, McCammon JA. PMID: 16683746.
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    363. Computing the Amino Acid Specificity of Fluctuations in Biomolecular Systems. J Chem Theory Comput. 2006 May; 2(3):873-8. Hamacher K, McCammon JA. PMID: 26626694.
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    364. A minimal model for stabilization of biomolecules by hydrocarbon cross-linking. J Chem Phys. 2006 Apr 28; 124(16):164907. Hamacher K, Hübsch A, McCammon JA. PMID: 16674170.
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    365. 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. Ung MU, Lu B, McCammon JA. PMID: 16365849.
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    366. Elasticity of peptide omega bonds. Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Apr; 73(4 Pt 1):041908. Shen T, Hamelberg D, McCammon JA. PMID: 16711837.
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    367. 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. Chang CE, Shen T, Trylska J, Tozzini V, McCammon JA. PMID: 16533835.
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    368. 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. Zhang D, Gullingsrud J, McCammon JA. PMID: 16506783.
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    369. 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. Cheng Y, Zhang Y, McCammon JA. PMID: 16522793.
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    370. Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models. Phys Rev Lett. 2006 Mar 03; 96(8):087802. Dzubiella J, Swanson JM, McCammon JA. PMID: 16606226.
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    371. Coupling nonpolar and polar solvation free energies in implicit solvent models. J Chem Phys. 2006 Feb 28; 124(8):084905. Dzubiella J, Swanson JM, McCammon JA. PMID: 16512740.
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    372. Dependency map of proteins in the small ribosomal subunit. PLoS Comput Biol. 2006 Feb; 2(2):e10. Hamacher K, Trylska J, McCammon JA. PMID: 16485038.
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    373. 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. Ivanov I, Vemparala S, Pophristic V, Kuroda K, DeGrado WF, McCammon JA, Klein ML. PMID: 16464062.
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    374. Conformational transitions in protein-protein association: binding of fasciculin-2 to acetylcholinesterase. Biophys J. 2006 May 01; 90(9):3280-7. Bui JM, Radic Z, Taylor P, McCammon JA. PMID: 16473897.
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    375. 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. Tozzini V, Rocchia W, McCammon JA. PMID: 19461947.
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    376. Dynamic binding of PKA regulatory subunit RI alpha. Structure. 2006 Jan; 14(1):141-9. Gullingsrud J, Kim C, Taylor SS, McCammon JA. PMID: 16407073.
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    377. Induced fit in mouse acetylcholinesterase upon binding a femtomolar inhibitor: a molecular dynamics study. J Med Chem. 2005 Dec 29; 48(26):8155-62. Senapati S, Bui JM, McCammon JA. PMID: 16366597.
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    378. Acetylcholinesterase: pivotal roles of its long omega loop (Cys69-Cys96) in regulating substrate binding. Chem Biol Interact. 2005 Dec 15; 157-158:357-9. Bui JM, McCammon JA. PMID: 16429484.
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    379. 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. Vigil D, Lin JH, Sotriffer CA, Pennypacker JK, McCammon JA, Taylor SS. PMID: 16322564.
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    380. Molecular docking of balanol to dynamics snapshots of protein kinase A. Proteins. 2005 Dec 01; 61(4):850-8. Wong CF, Kua J, Zhang Y, Straatsma TP, McCammon JA. PMID: 16245317.
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    381. The association of tetrameric acetylcholinesterase with ColQ tail: a block normal mode analysis. PLoS Comput Biol. 2005 Nov; 1(6):e62. Zhang D, McCammon JA. PMID: 16299589.
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    382. 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. Giorgione JR, Lin JH, McCammon JA, Newton AC. PMID: 16293612.
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    383. Channel opening motion of alpha7 nicotinic acetylcholine receptor as suggested by normal mode analysis. J Mol Biol. 2006 Jan 13; 355(2):310-24. Cheng X, Lu B, Grant B, Law RJ, McCammon JA. PMID: 16307758.
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    384. Potent, selective pyrone-based inhibitors of stromelysin-1. J Am Chem Soc. 2005 Oct 19; 127(41):14148-9. Puerta DT, Mongan J, Tran BL, McCammon JA, Cohen SM. PMID: 16218585.
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    385. 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. Hamelberg D, McCammon JA. PMID: 16201784.
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    386. Target flexibility in molecular recognition. Biochim Biophys Acta. 2005 Dec 30; 1754(1-2):221-4. McCammon JA. PMID: 16181817.
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    387. The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain. FASEB J. 2005 Sep; 19(11):1389-95. Shen T, Zong C, Hamelberg D, McCammon JA, Wolynes PG. PMID: 16126906.
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    388. 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. Lu B, Cheng X, Hou T, McCammon JA. PMID: 16164327.
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    389. The entropic cost of protein-protein association: a case study on acetylcholinesterase binding to fasciculin-2. Biophys J. 2005 Oct; 89(4):L25-7. Minh DD, Bui JM, Chang CE, Jain T, Swanson JM, McCammon JA. PMID: 16100267.
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    390. Limitations of atom-centered dielectric functions in implicit solvent models. J Phys Chem B. 2005 Aug 11; 109(31):14769-72. Swanson JM, Mongan J, McCammon JA. PMID: 16852866.
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    391. Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach. J Am Chem Soc. 2005 Aug 10; 127(31):11125-33. Trylska J, McCammon JA, Brooks Iii CL. PMID: 16076220.
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    392. Exploring global motions and correlations in the ribosome. Biophys J. 2005 Sep; 89(3):1455-63. Trylska J, Tozzini V, McCammon JA. PMID: 15951386.
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    393. 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. Lu B, Zhang D, McCammon JA. PMID: 15974723.
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    394. Substrate concentration dependence of the diffusion-controlled steady-state rate constant. J Chem Phys. 2005 May 08; 122(18):184902. Dzubiella J, McCammon JA. PMID: 15918760.
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    395. Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems. J Comput Chem. 2005 May; 26(7):668-81. Sims PA, Wong CF, Vuga D, McCammon JA, Sefton BM. PMID: 15754303.
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    396. Optimized Radii for Poisson-Boltzmann Calculations with the AMBER Force Field. J Chem Theory Comput. 2005 May; 1(3):484-93. Swanson JM, Adcock SA, McCammon JA. PMID: 26641515.
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    397. 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. Law RJ, Henchman RH, McCammon JA. PMID: 15857954.
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    398. 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. Hamelberg D, Shen T, McCammon JA. PMID: 15701032.
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    399. 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. Cheng Y, Zhang Y, McCammon JA. PMID: 15686389.
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    400. Ligand-induced conformational change in the alpha7 nicotinic receptor ligand binding domain. Biophys J. 2005 Apr; 88(4):2564-76. Henchman RH, Wang HL, Sine SM, Taylor P, McCammon JA. PMID: 15665135.
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    401. Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation study. Protein Sci. 2005 Jan; 14(1):159-68. Lu B, Wong CF, McCammon JA. PMID: 15608120.
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    402. Rapid Estimation of Solvation Energy for Simulations of Protein-Protein Association. J Chem Theory Comput. 2005 Jan; 1(1):143-52. Cerutti DS, Ten Eyck LF, McCammon JA. PMID: 26641125.
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    403. 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. Zhang D, Suen J, Zhang Y, Song Y, Radic Z, Taylor P, Holst MJ, Bajaj C, Baker NA, McCammon JA. PMID: 15626705.
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    404. 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. Gao F, Bren N, Burghardt TP, Hansen S, Henchman RH, Taylor P, McCammon JA, Sine SM. PMID: 15591050.
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    405. Constant pH molecular dynamics in generalized Born implicit solvent. J Comput Chem. 2004 Dec; 25(16):2038-48. Mongan J, Case DA, McCammon JA. PMID: 15481090.
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    406. 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. Zhang D, Konecny R, Baker NA, McCammon JA. PMID: 15386271.
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    407. Finite concentration effects on diffusion-controlled reactions. J Chem Phys. 2004 Oct 22; 121(16):7896-900. Senapati S, Wong CF, McCammon JA. PMID: 15485251.
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    408. Ribosome motions modulate electrostatic properties. Biopolymers. 2004 Aug 15; 74(6):423-31. Trylska J, Konecny R, Tama F, Brooks CL, McCammon JA. PMID: 15274086.
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    409. Charge optimization of the interface between protein kinases and their ligands. J Comput Chem. 2004 Aug; 25(11):1416-29. Sims PA, Wong CF, McCammon JA. PMID: 15185335.
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    410. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 2004 Jul 01; 32(Web Server issue):W665-7. Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PMID: 15215472.
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    411. 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. Hamelberg D, McCammon JA. PMID: 15198616.
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    412. Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J Chem Phys. 2004 Jun 22; 120(24):11919-29. Hamelberg D, Mongan J, McCammon JA. PMID: 15268227.
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    413. 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. Bui JM, Tai K, McCammon JA. PMID: 15186156.
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    414. Discovery of a novel binding trench in HIV integrase. J Med Chem. 2004 Apr 08; 47(8):1879-81. Schames JR, Henchman RH, Siegel JS, Sotriffer CA, Ni H, McCammon JA. PMID: 15055986.
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    415. 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. Perryman AL, Lin JH, McCammon JA. PMID: 15044738.
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    416. Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophys J. 2004 Apr; 86(4):2017-29. Song Y, Zhang Y, Shen T, Bajaj CL, McCammon JA, Baker NA. PMID: 15041644.
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    417. The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease. Protein Sci. 2004 Feb; 13(2):513-28. Trylska J, Grochowski P, McCammon JA. PMID: 14739332.
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    418. 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. Swanson JM, Henchman RH, McCammon JA. PMID: 14695250.
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    419. 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. Kua J, Zhang Y, Eslami AC, Butler JR, McCammon JA. PMID: 14627729.
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    420. 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. Henchman RH, Wang HL, Sine SM, Taylor P, McCammon JA. PMID: 14581202.
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    421. The physical basis of microtubule structure and stability. Protein Sci. 2003 Oct; 12(10):2257-61. Sept D, Baker NA, McCammon JA. PMID: 14500883.
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    422. Brownian dynamics simulation of helix-capping motifs. Biopolymers. 2003 Oct; 70(2):252-9. Shen T, Wong CF, McCammon JA. PMID: 14517913.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    423. Brownian dynamics simulations of ion atmospheres around polyalanine and B-DNA: effects of biomolecular dielectric. Biopolymers. 2003 Oct; 70(3):391-402. Cerutti DS, Wong CF, McCammon JA. PMID: 14579311.
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    424. The dynamics of ligand barrier crossing inside the acetylcholinesterase gorge. Biophys J. 2003 Oct; 85(4):2267-72. Bui JM, Henchman RH, McCammon JA. PMID: 14507691.
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    425. The pH dependence of stability of the activation helix and the catalytic site of GART. Biophys Chem. 2003 Sep; 105(2-3):279-91. Morikis D, Elcock AH, Jennings PA, McCammon JA. PMID: 14499900.
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    426. Calculating pKa values in enzyme active sites. Protein Sci. 2003 Sep; 12(9):1894-901. Nielsen JE, McCammon JA. PMID: 12930989.
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    427. 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. Puerta DT, Schames JR, Henchman RH, McCammon JA, Cohen SM. PMID: 12923840.
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    428. A computational model of binding thermodynamics: the design of cyclin-dependent kinase 2 inhibitors. J Med Chem. 2003 Jul 17; 46(15):3314-25. Sims PA, Wong CF, McCammon JA. PMID: 12852762.
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    429. Nanosecond dynamics of the mouse acetylcholinesterase cys69-cys96 omega loop. J Biol Chem. 2003 Aug 15; 278(33):30905-11. Shi J, Tai K, McCammon JA, Taylor P, Johnson DA. PMID: 12759360.
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    430. Finite element simulations of acetylcholine diffusion in neuromuscular junctions. Biophys J. 2003 Apr; 84(4):2234-41. Tai K, Bond SD, MacMillan HR, Baker NA, Holst MJ, McCammon JA. PMID: 12668432.
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    431. On the evaluation and optimization of protein X-ray structures for pKa calculations. Protein Sci. 2003 Feb; 12(2):313-26. Nielsen JE, McCammon JA. PMID: 12538895.
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    432. Electrostatic interactions. Methods Biochem Anal. 2003; 44:427-40. Baker NA, McCammon JA. PMID: 12647398.
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    433. The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers. 2003 Jan; 68(1):47-62. Lin JH, Perryman AL, Schames JR, McCammon JA. PMID: 12579579.
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    434. Modeling HIV-1 integrase complexes based on their hydrodynamic properties. Biopolymers. 2003 Jan; 68(1):110-20. Podtelezhnikov AA, Gao K, Bushman FD, McCammon JA. PMID: 12579583.
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    435. 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. Perryman AL, McCammon JA. PMID: 12477345.
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    436. Thalassiolins A-C: new marine-derived inhibitors of HIV cDNA integrase. Bioorg Med Chem. 2002 Nov; 10(11):3619-25. Rowley DC, Hansen MS, Rhodes D, Sotriffer CA, Ni H, McCammon JA, Bushman FD, Fenical W. PMID: 12213478.
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    437. 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. Zhang Y, Kua J, McCammon JA. PMID: 12197759.
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    438. Bridging implicit and explicit solvent approaches for membrane electrostatics. Biophys J. 2002 Sep; 83(3):1374-9. Lin JH, Baker NA, McCammon JA. PMID: 12202363.
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    439. Structural and dynamic properties of water around acetylcholinesterase. Protein Sci. 2002 Sep; 11(9):2080-90. Henchman RH, McCammon JA. PMID: 12192064.
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    440. Molecular dynamics simulations of biomolecules. Nat Struct Biol. 2002 Sep; 9(9):646-52. Karplus M, McCammon JA. PMID: 12198485.
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    441. 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. Shen T, Canino LS, McCammon JA. PMID: 12190614.
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    442. 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. Kua J, Zhang Y, McCammon JA. PMID: 12105904.
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    443. Extracting hydration sites around proteins from explicit water simulations. J Comput Chem. 2002 Jul 15; 23(9):861-9. Henchman RH, McCammon JA. PMID: 11984847.
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    444. Molecular dynamics of acetylcholinesterase. Acc Chem Res. 2002 Jun; 35(6):332-40. Shen T, Tai K, Henchman RH, McCammon JA. PMID: 12069617.
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    445. Mechanism of acetylcholinesterase inhibition by fasciculin: a 5-ns molecular dynamics simulation. J Am Chem Soc. 2002 May 29; 124(21):6153-61. Tai K, Shen T, Henchman RH, Bourne Y, Marchot P, McCammon JA. PMID: 12022850.
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    446. Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J Am Chem Soc. 2002 May 22; 124(20):5632-3. Lin JH, Perryman AL, Schames JR, McCammon JA. PMID: 12010024.
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    447. Properties of water molecules in the active site gorge of acetylcholinesterase from computer simulation. Biophys J. 2002 May; 82(5):2671-82. Henchman RH, Tai K, Shen T, McCammon JA. PMID: 11964254.
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    448. Binding of aminoglycoside antibiotics to the small ribosomal subunit: a continuum electrostatics investigation. J Am Chem Soc. 2002 Feb 20; 124(7):1438-42. Ma C, Baker NA, Joseph S, McCammon JA. PMID: 11841313.
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    449. Protein flexibility and computer-aided drug design. Annu Rev Pharmacol Toxicol. 2003; 43:31-45. Wong CF, McCammon JA. PMID: 12142469.
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    450. 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. Morikis D, Elcock AH, Jennings PA, McCammon JA. PMID: 11604542.
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    451. Proton transfer dynamics of GART: the pH-dependent catalytic mechanism examined by electrostatic calculations. Protein Sci. 2001 Nov; 10(11):2379-92. Morikis D, Elcock AH, Jennings PA, McCammon JA. PMID: 11604543.
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    452. Kinetic mechanism of end-to-end annealing of actin filaments. J Mol Biol. 2001 Sep 28; 312(4):721-30. Andrianantoandro E, Blanchoin L, Sept D, McCammon JA, Pollard TD. PMID: 11575927.
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    453. Atomistic Brownian dynamics simulation of peptide phosphorylation. J Am Chem Soc. 2001 Sep 19; 123(37):9107-11. Shen T, Wong CF, McCammon JA. PMID: 11552818.
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    454. 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. Ni H, Sotriffer CA, McCammon JA. PMID: 11543671.
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    455. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A. 2001 Aug 28; 98(18):10037-41. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. PMID: 11517324.
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    456. Thermodynamics and kinetics of actin filament nucleation. Biophys J. 2001 Aug; 81(2):667-74. Sept D, McCammon JA. PMID: 11463615.
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    457. Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase. Biophys J. 2001 Aug; 81(2):715-24. Tai K, Shen T, Börjesson U, Philippopoulos M, McCammon JA. PMID: 11463620.
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    458. Computational analysis of PKA-balanol interactions. J Med Chem. 2001 May 10; 44(10):1530-9. Wong CF, Hünenberger PH, Akamine P, Narayana N, Diller T, McCammon JA, Taylor S, Xuong NH. PMID: 11334563.
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    459. A model for enzyme-substrate interaction in alanine racemase. J Am Chem Soc. 2001 Mar 28; 123(12):2830-4. Ondrechen MJ, Briggs JM, McCammon JA. PMID: 11456969.
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    460. 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. Shen TY, Tai K, McCammon JA. PMID: 11308872.
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    461. Calculation of weak protein-protein interactions: the pH dependence of the second virial coefficient. Biophys J. 2001 Feb; 80(2):613-25. Elcock AH, McCammon JA. PMID: 11159430.
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    462. The structure of Sky1p reveals a novel mechanism for constitutive activity. Nat Struct Biol. 2001 Feb; 8(2):176-83. Nolen B, Yun CY, Wong CF, McCammon JA, Fu XD, Ghosh G. PMID: 11175909.
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    463. Active site binding modes of HIV-1 integrase inhibitors. J Med Chem. 2000 Nov 02; 43(22):4109-17. Sotriffer CA, Ni H, McCammon JA. PMID: 11063607.
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    464. Quantum-dynamical picture of a multistep enzymatic process: reaction catalyzed by phospholipase A(2). Biophys J. 2000 Sep; 79(3):1253-62. Bala P, Grochowski P, Nowinski K, Lesyng B, McCammon JA. PMID: 10968989.
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    465. Developing a dynamic pharmacophore model for HIV-1 integrase. J Med Chem. 2000 Jun 01; 43(11):2100-14. Carlson HA, Masukawa KM, Rubins K, Bushman FD, Jorgensen WL, Lins RD, Briggs JM, McCammon JA. PMID: 10841789.
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    466. 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. Brown FL, Leitner DM, McCammon JA, Wilson KR. PMID: 10777724.
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    467. Electrostatic steering of substrate to acetylcholinesterase: analysis of field fluctuations. Biopolymers. 2000 Mar; 53(3):265-71. Wlodek ST, Shen T, McCammon JA. PMID: 10679631.
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    468. Accommodating protein flexibility in computational drug design. Mol Pharmacol. 2000 Feb; 57(2):213-8. Carlson HA, McCammon JA. PMID: 10648630.
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    469. Computer simulations of actin polymerization can explain the barbed-pointed end asymmetry. J Mol Biol. 1999 Dec 17; 294(5):1181-9. Sept D, Elcock AH, McCammon JA. PMID: 10600376.
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    470. Annealing accounts for the length of actin filaments formed by spontaneous polymerization. Biophys J. 1999 Dec; 77(6):2911-9. Sept D, Xu J, Pollard TD, McCammon JA. PMID: 10585915.
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    471. Molecular dynamics of mouse acetylcholinesterase complexed with huperzine A. Biopolymers. 1999 Oct 05; 50(4):347-59. Tara S, Helms V, Straatsma TP, McCammon JA. PMID: 10423544.
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    472. Dynamical properties of fasciculin-2. Proteins. 1999 Sep 01; 36(4):447-53. Baker NA, Helms V, McCammon JA. PMID: 10450086.
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    473. Computer simulation of protein-protein association kinetics: acetylcholinesterase-fasciculin. J Mol Biol. 1999 Aug 06; 291(1):149-62. Elcock AH, Gabdoulline RR, Wade RC, McCammon JA. PMID: 10438612.
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    474. Mouse acetylcholinesterase unliganded and in complex with huperzine A: a comparison of molecular dynamics simulations. Biopolymers. 1999 Jul; 50(1):35-43. Tara S, Straatsma TP, McCammon JA. PMID: 10341665.
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    475. Molecular dynamics studies on the HIV-1 integrase catalytic domain. Biophys J. 1999 Jun; 76(6):2999-3011. Lins RD, Briggs JM, Straatsma TP, Carlson HA, Greenwald J, Choe S, McCammon JA. PMID: 10354426.
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    476. 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. Weber W, Helms V, McCammon JA, Langhoff PW. PMID: 10339561.
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    477. 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. Hünenberger PH, McCammon JA. PMID: 10343384.
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    478. 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. Wriggers W, Milligan RA, McCammon JA. PMID: 10222274.
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    479. Phosphorylation stabilizes the N-termini of alpha-helices. Biopolymers. 1999 Mar; 49(3):225-33. Smart JL, McCammon JA. PMID: 9990840.
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    480. Determinants of ligand binding to cAMP-dependent protein kinase. Biochemistry. 1999 Feb 23; 38(8):2358-66. Hünenberger PH, Helms V, Narayana N, Taylor SS, McCammon JA. PMID: 10029529.
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    481. 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. de Bakker PI, Hünenberger PH, McCammon JA. PMID: 9917414.
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    482. 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. Carlson HA, Briggs JM, McCammon JA. PMID: 9888837.
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    483. Poisson-Boltzmann model studies of molecular electrostatic properties of the cAMP-dependent protein kinase. Eur Biophys J. 1999; 28(6):457-67. Blachut-Okrasinska E, Lesyng B, Briggs JM, McCammon JA, Antosiewicz JM. PMID: 10460339.
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    484. Self-organizing neural networks bridge the biomolecular resolution gap. J Mol Biol. 1998 Dec 18; 284(5):1247-54. Wriggers W, Milligan RA, Schulten K, McCammon JA. PMID: 9878345.
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    485. 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. Tara S, Elcock AH, Kirchhoff PD, Briggs JM, Radic Z, Taylor P, McCammon JA. PMID: 9838872.
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    486. Brownian and essential dynamics studies of the HIV-1 integrase catalytic domain. J Biomol Struct Dyn. 1998 Dec; 16(3):733-45. Weber W, Demirdjian H, Lins RD, Briggs JM, Ferreira R, McCammon JA. PMID: 10052629.
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    487. Analysis of synaptic transmission in the neuromuscular junction using a continuum finite element model. Biophys J. 1998 Oct; 75(4):1679-88. Smart JL, McCammon JA. PMID: 9746510.
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    488. Conformation gating as a mechanism for enzyme specificity. Proc Natl Acad Sci U S A. 1998 Aug 04; 95(16):9280-3. Zhou HX, Wlodek ST, McCammon JA. PMID: 9689071.
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    489. Electrostatic contributions to the stability of halophilic proteins. J Mol Biol. 1998 Jul 24; 280(4):731-48. Elcock AH, McCammon JA. PMID: 9677300.
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    490. Theory of biomolecular recognition. Curr Opin Struct Biol. 1998 Apr; 8(2):245-9. McCammon JA. PMID: 9631300.
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    491. Correlation between rate of enzyme-substrate diffusional encounter and average Boltzmann factor around active site. Biopolymers. 1998 Apr; 45(5):355-60. Zhou HX, Briggs JM, Tara S, McCammon JA. PMID: 9530014.
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    492. 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. Marrone TJ, Resat H, Hodge CN, Chang CH, McCammon JA. PMID: 9541388.
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    493. Electrostatic channeling of substrates between enzyme active sites: comparison of simulation and experiment. Biochemistry. 1997 Dec 23; 36(51):16049-58. Elcock AH, Huber GA, McCammon JA. PMID: 9405038.
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    494. pH dependence of antibody/lysozyme complexation. Biochemistry. 1997 Dec 16; 36(50):15599-614. Gibas CJ, Subramaniam S, McCammon JA, Braden BC, Poljak RJ. PMID: 9398288.
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    495. Kinase conformations: a computational study of the effect of ligand binding. Protein Sci. 1997 Nov; 6(11):2336-43. Helms V, McCammon JA. PMID: 9385635.
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    496. Molecular properties of amphotericin B membrane channel: a molecular dynamics simulation. Mol Pharmacol. 1997 Oct; 52(4):560-70. Baginski M, Resat H, McCammon JA. PMID: 9380018.
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    497. 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. Radic Z, Kirchhoff PD, Quinn DM, McCammon JA, Taylor P. PMID: 9287336.
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    498. Colloquium on signaling and molecular structure in pharmacology (La Jolla, California, March 11-12, 1997). Mol Pharmacol. 1997 Jul; 52(1):1-5. Taylor P, Ross EM, Sternweis PC, Neubig RR, McCammon JA. PMID: 9224805.
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    499. Modeling the electrophoresis of lysozyme. II. Inclusion of ion relaxation. Biophys J. 1997 Jul; 73(1):133-40. Allison SA, Potter M, McCammon JA. PMID: 9199778.
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