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J. Andrew McCammon - Publications

Affiliations: 
University of California, San Diego, La Jolla, CA 
Area:
Statistical mechanics and computational chemistry, with applications to biological systems
Website:
http://www-chem.ucsd.edu/faculty/profiles/mccammon_james_a.html

500 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Mindrebo JT, Patel A, Kim WE, Davis TD, Chen A, Bartholow TG, La Clair JJ, McCammon JA, Noel JP, Burkart MD. Gating mechanism of elongating β-ketoacyl-ACP synthases. Nature Communications. 11: 1727. PMID 32265440 DOI: 10.1038/s41467-020-15455-x  0.4
2020 Lee CT, Laughlin JG, Angliviel de La Beaumelle N, Amaro RE, McCammon JA, Ramamoorthi R, Holst M, Rangamani P. 3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries. Plos Computational Biology. 16: e1007756. PMID 32251448 DOI: 10.1371/journal.pcbi.1007756  0.96
2020 Lee CT, Laughlin JG, Moody JB, Amaro RE, McCammon JA, Holst M, Rangamani P. An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries. Biophysical Journal. PMID 32032503 DOI: 10.1016/j.bpj.2019.11.3400  0.96
2019 Huber GA, McCammon JA. Brownian Dynamics Simulations of Biological Molecules. Trends in Chemistry. 1: 727-738. PMID 32309795 DOI: 10.1016/j.trechm.2019.07.008  0.6
2019 Aboelkassem Y, McCabe KJ, Huber GA, Regnier M, McCammon JA, McCulloch AD. A Stochastic Multiscale Model of Cardiac Thin Filament Activation Using Brownian-Langevin Dynamics. Biophysical Journal. PMID 31547973 DOI: 10.1016/j.bpj.2019.08.003  0.6
2019 Palermo G, Ricci CG, McCammon JA. The invisible dance of CRISPR-Cas9. Simulations unveil the molecular side of the gene-editing revolution. Physics Today. 72: 30-36. PMID 31511751 DOI: 10.1063/PT.3.4182  0.88
2019 Lee CT, Moody JB, Amaro RE, McCammon JA, Holst MJ. The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation. Acm Transactions On Mathematical Software. Association For Computing Machinery. 45. PMID 31474782 DOI: 10.1145/3321515  0.96
2019 Sztain-Pedone T, Bartholow T, McCammon JA, Burkart MD. Shifting the Hydrolysis Equilibrium of Substrate Loaded Acyl Carrier Proteins. Biochemistry. PMID 31397556 DOI: 10.1021/acs.biochem.9b00612  0.4
2019 Zhou S, Weiß RG, Cheng LT, Dzubiella J, McCammon JA, Li B. Variational implicit-solvent predictions of the dry-wet transition pathways for ligand-receptor binding and unbinding kinetics. Proceedings of the National Academy of Sciences of the United States of America. PMID 31270236 DOI: 10.1073/pnas.1902719116  1
2019 Sztain T, Patel A, Lee DJ, Davis T, McCammon JA, Burkart MD. One atom matters: modifying the thioester linkage affects structure of the acyl carrier protein. Angewandte Chemie (International Ed. in English). PMID 31140212 DOI: 10.1002/anie.201903815  0.4
2019 Ricci CG, Chen JS, Miao Y, Jinek M, Doudna JA, McCammon JA, Palermo G. Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics. Acs Central Science. 5: 651-662. PMID 31041385 DOI: 10.1021/acscentsci.9b00020  0.88
2019 Dodge GJ, Patel A, Jaremko KL, McCammon JA, Smith JL, Burkart MD. Structural and dynamical rationale for fatty acid unsaturation in . Proceedings of the National Academy of Sciences of the United States of America. PMID 30872475 DOI: 10.1073/pnas.1818686116  0.4
2019 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, ... ... McCammon JA, et al. Allostery in Its Many Disguises: From Theory to Applications. Structure (London, England : 1993). PMID 30744993 DOI: 10.1016/j.str.2019.01.003  0.88
2018 Fang F, Huang J, Huber G, McCammon JA, Zhang BO. HIERARCHICAL ORTHOGONAL MATRIX GENERATION AND MATRIX-VECTOR MULTIPLICATIONS IN RIGID BODY SIMULATIONS. Siam Journal On Scientific Computing : a Publication of the Society For Industrial and Applied Mathematics. 40: A1345-A1361. PMID 31452593 DOI: 10.1137/17M1117744  0.84
2018 Palermo G, Chen JS, Ricci CG, Rivalta I, Jinek M, Batista VS, Doudna JA, McCammon JA. Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain. Quarterly Reviews of Biophysics. 51: e9. PMID 30912489 DOI: 10.1017/S0033583518000070  0.88
2018 Feher VA, Schiffer JM, Mermelstein DJ, Mih N, Pierce LCT, McCammon JA, Amaro RE. Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant. Biophysical Journal. PMID 30606449 DOI: 10.1016/j.bpj.2018.09.035  0.96
2018 Huang YM, Munguia J, Miao Y, Nizet V, McCammon JA. Docking simulation and antibiotic discovery targeting the MlaC protein in Gram-negative bacteria. Chemical Biology & Drug Design. PMID 30570806 DOI: 10.1111/cbdd.13462  0.88
2018 Palermo G, Chen JS, Ricci CG, Rivalta I, Jinek M, Batista VS, Doudna JA, McCammon JA. Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain. Quarterly Reviews of Biophysics. 51. PMID 30555184 DOI: 10.1017/S0033583518000070  0.88
2018 Zhang J, Wang N, Miao Y, Hauser F, McCammon JA, Rappel WJ, Schroeder JI. Identification of SLAC1 anion channel residues required for CO/bicarbonate sensing and regulation of stomatal movements. Proceedings of the National Academy of Sciences of the United States of America. PMID 30301791 DOI: 10.1073/pnas.1807624115  0.88
2018 Utesch T, de Miguel Catalina A, Schattenberg C, Paege N, Schmieder P, Krause E, Miao Y, McCammon JA, Meyer V, Jung S, Mroginski MA. A Computational Modeling Approach Predicts Interaction of the Antifungal Protein AFP from with Fungal Membranes via Its γ-Core Motif. Msphere. 3. PMID 30282755 DOI: 10.1128/mSphere.00377-18  0.88
2018 Mermelstein DJ, McCammon JA, Walker RC. pH-dependent conformational dynamics of beta-secretase 1: A molecular dynamics study. Journal of Molecular Recognition : Jmr. e2765. PMID 30264484 DOI: 10.1002/jmr.2765  0.64
2018 G Ricci C, McCammon JA. Heterogeneous Solvation in Distinctive Protein-Protein Interfaces Revealed by Molecular Dynamics Simulations. The Journal of Physical Chemistry. B. PMID 30252476 DOI: 10.1021/acs.jpcb.8b07773  0.8
2018 Amaro RE, Baudry J, Chodera J, Demir Ö, McCammon JA, Miao Y, Smith JC. Ensemble Docking in Drug Discovery. Biophysical Journal. PMID 29606412 DOI: 10.1016/j.bpj.2018.02.038  0.96
2018 Mermelstein DJ, Lin C, Nelson G, Kretsch R, McCammon JA, Walker RC. Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package. Journal of Computational Chemistry. PMID 29532496 DOI: 10.1002/jcc.25187  0.64
2018 Miao Y, McCammon JA. Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor. Proceedings of the National Academy of Sciences of the United States of America. PMID 29507218 DOI: 10.1073/pnas.1800756115  0.88
2018 Huang YM, McCammon JA, Miao Y. Replica exchange Gaussian accelerated molecular dynamics: Improved enhanced sampling and free energy calculation. Journal of Chemical Theory and Computation. PMID 29489349 DOI: 10.1021/acs.jctc.7b01226  0.88
2018 Ricci CG, Li B, Cheng LT, Dzubiella J, McCammon JA. Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly. Frontiers in Molecular Biosciences. 5: 13. PMID 29484300 DOI: 10.3389/fmolb.2018.00013  1
2018 Miao Y, Huang YM, Walker RC, McCammon JA, Chang CA. Ligand Binding Pathways and Conformational Transitions of the HIV Protease. Biochemistry. PMID 29394043 DOI: 10.1021/acs.biochem.7b01248  0.88
2018 Mouchlis VD, Chen Y, McCammon JA, Dennis EA. Membrane Allostery and Unique Hydrophobic Sites Promote Enzyme Substrate Specificity. Journal of the American Chemical Society. PMID 29342349 DOI: 10.1021/jacs.7b12045  0.4
2017 Miao Y, McCammon JA. Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications. Annual Reports in Computational Chemistry. 13: 231-278. PMID 29720925 DOI: 10.1016/bs.arcc.2017.06.005  0.88
2017 Huang YM, Huber GA, Wang N, Minteer SD, McCammon JA. Brownian dynamic study of an enzyme metabolon in the TCA cycle: Substrate kinetics and channeling. Protein Science : a Publication of the Protein Society. PMID 29094409 DOI: 10.1002/pro.3338  0.88
2017 Jaremko MJ, Lee DJ, Patel A, Winslow V, Opella SJ, McCammon JA, Burkart MD. Manipulating protein-protein interactions in NRPS type II PCPs. Biochemistry. PMID 28920687 DOI: 10.1021/acs.biochem.7b00884  0.4
2017 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, ... ... McCammon JA, et al. Improvements to the APBS biomolecular solvation software suite. Protein Science : a Publication of the Protein Society. PMID 28836357 DOI: 10.1002/pro.3280  0.96
2017 Palermo G, G Ricci C, Fernando A, Basak R, Jinek M, Rivalta I, Batista VS, McCammon JA. PAM-induced allostery activates CRISPR-Cas9. Journal of the American Chemical Society. PMID 28764328 DOI: 10.1021/jacs.7b05313  0.88
2017 Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Proceedings of the National Academy of Sciences of the United States of America. PMID 28652374 DOI: 10.1073/pnas.1707645114  0.88
2017 Caliman AD, Miao Y, McCammon JA. Mapping the Allosteric Sites of the A2A Adenosine Receptor. Chemical Biology & Drug Design. PMID 28639411 DOI: 10.1111/cbdd.13053  0.88
2017 Gravina Ricci C, Li B, Cheng LT, Dzubiella J, McCammon JA. 'Martinizing' the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins. The Journal of Physical Chemistry. B. PMID 28613904 DOI: 10.1021/acs.jpcb.7b04113  1
2017 Dick BL, Patel A, McCammon JA, Cohen SM. Effect of donor atom identity on metal-binding pharmacophore coordination. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. PMID 28389830 DOI: 10.1007/s00775-017-1454-3  0.52
2017 Caliman AD, Miao Y, McCammon JA. Activation Mechanisms of the First Sphingosine-1-Phosphate Receptor. Protein Science : a Publication of the Protein Society. PMID 28370663 DOI: 10.1002/pro.3165  0.88
2017 O'Dowd B, Williams S, Wang H, No JH, Rao G, Wang W, McCammon JA, Cramer SP, Oldfield E. Spectroscopic and Computational Investigations of Ligand Binding to IspH: Discovery of Non-Diphosphate Inhibitors. Chembiochem : a European Journal of Chemical Biology. PMID 28253432 DOI: 10.1002/cbic.201700052  0.8
2017 O'Dowd B, Williams S, Wang H, No JH, Rao G, Wang W, McCammon JA, Cramer SP, Oldfield E. Inside Cover: Spectroscopic and Computational Investigations of Ligand Binding to IspH: Discovery of Non-diphosphate Inhibitors (ChemBioChem 10/2017) Chembiochem. 18: 882-882. DOI: 10.1002/cbic.201700218  0.8
2016 Pang YT, Miao Y, Wang Y, McCammon JA. Gaussian Accelerated Molecular Dynamics in NAMD. Journal of Chemical Theory and Computation. PMID 28034310 DOI: 10.1021/acs.jctc.6b00931  0.88
2016 Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations. Acs Central Science. 2: 756-763. PMID 27800559 DOI: 10.1021/acscentsci.6b00218  0.88
2016 Miao Y, McCammon JA. Graded activation and free energy landscapes of a muscarinic G-protein-coupled receptor. Proceedings of the National Academy of Sciences of the United States of America. 113: 12162-12167. PMID 27791003 DOI: 10.1073/pnas.1614538113  0.88
2016 Miao Y, Goldfeld DA, Moo EV, Sexton PM, Christopoulos A, McCammon JA, Valant C. Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor. Proceedings of the National Academy of Sciences of the United States of America. 113: E5675-84. PMID 27601651 DOI: 10.1073/pnas.1612353113  0.88
2016 G Ricci C, Liu YL, Zhang Y, Wang Y, Zhu W, Oldfield E, McCammon JA. Dynamic Structure and Inhibition of a Malaria Drug Target: Geranylgeranyl Diphosphate Synthase. Biochemistry. 55: 5180-90. PMID 27564465 DOI: 10.1021/acs.biochem.6b00398  1
2016 Zhou S, Sun H, Cheng LT, Dzubiella J, Li B, McCammon JA. Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations. The Journal of Chemical Physics. 145: 054114. PMID 27497546 DOI: 10.1063/1.4959971  1
2016 Miao Y, McCammon JA. Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review. Molecular Simulation. 42: 1046-1055. PMID 27453631 DOI: 10.1080/08927022.2015.1121541  0.88
2016 Miao Y, McCammon JA. G-protein coupled receptors: advances in simulation and drug discovery. Current Opinion in Structural Biology. 41: 83-89. PMID 27344006 DOI: 10.1016/j.sbi.2016.06.008  0.88
2016 Mouchlis VD, Morisseau C, Hammock BD, Li S, McCammon JA, Dennis EA. Computer-aided drug design guided by hydrogen/deuterium exchange mass spectrometry: A powerful combination for the development of potent and selective inhibitors of Group VIA calcium-independent phospholipase A2. Bioorganic & Medicinal Chemistry. 24: 4801-4811. PMID 27320659 DOI: 10.1016/j.bmc.2016.05.009  0.4
2016 Huber GA, Miao Y, Zhou S, Li B, McCammon JA. Hybrid finite element and Brownian dynamics method for charged particles. The Journal of Chemical Physics. 144: 164107. PMID 27131531 DOI: 10.1063/1.4947086  0.88
2016 Huang YM, Miao Y, Munguia J, Lin L, Nizet V, McCammon JA. Molecular dynamic study of MlaC protein in Gram-negative bacteria: conformational flexibility, solvent effect and protein-phospholipid binding. Protein Science : a Publication of the Protein Society. 25: 1430-7. PMID 27111825 DOI: 10.1002/pro.2939  0.88
2016 Mouchlis VD, Limnios D, Kokotou MG, Barbayianni E, Kokotos G, McCammon JA, Dennis EA. Development of Potent and Selective Inhibitors for Group VIA Calcium-Independent Phospholipase A2 Guided by Molecular Dynamics and Structure-Activity Relationships. Journal of Medicinal Chemistry. 59: 4403-14. PMID 27087127 DOI: 10.1021/acs.jmedchem.6b00377  0.4
2016 Miao Y, Feixas F, Eun C, McCammon JA. Accelerated Molecular Dynamics Simulations of Protein Folding. Journal of Computational Chemistry. 37. PMID 26860347 DOI: 10.1002/jcc.24337  0.88
2016 Miao Y, Baudry J, Smith JC, McCammon JA. General trends of dihedral conformational transitions in a globular protein. Proteins. 84: 501-14. PMID 26799251 DOI: 10.1002/prot.24996  0.88
2016 Kim MO, McCammon JA. Computation of pH-dependent binding free energies. Biopolymers. 105: 43-9. PMID 26202905 DOI: 10.1002/bip.22702  0.68
2016 Wang N, McCammon JA. Substrate channeling between the human dihydrofolate reductase and thymidylate synthase. Protein Science : a Publication of the Protein Society. 25: 79-86. PMID 26096018 DOI: 10.1002/pro.2720  0.88
2016 Kim MO, McCammon JA. Computation of pH-dependent binding free energies Biopolymers. 105: 43-49. DOI: 10.1002/bip.22702  0.68
2015 Sun H, Wen J, Zhao Y, Li B, McCammon JA. A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics. The Journal of Chemical Physics. 143: 243110. PMID 26723595 DOI: 10.1063/1.4932336  0.8
2015 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, et al. Antiinfectives targeting enzymes and the proton motive force. Proceedings of the National Academy of Sciences of the United States of America. 112: E7073-82. PMID 26644565 DOI: 10.1073/pnas.1521988112  0.8
2015 Kappel K, Miao Y, McCammon JA. Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor. Quarterly Reviews of Biophysics. 48: 479-87. PMID 26537408 DOI: 10.1017/S0033583515000153  0.88
2015 Kim MO, Blachly PG, McCammon JA. Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria. Plos Computational Biology. 11: e1004341. PMID 26506513 DOI: 10.1371/journal.pcbi.1004341  0.68
2015 Cheng Y, Rao V, Tu AY, Lindert S, Wang D, Oxenford L, McCulloch AD, McCammon JA, Regnier M. Troponin I Mutations R146G and R21C Alter Cardiac Troponin Function, Contractile Properties, and Modulation by Protein Kinase A (PKA)-mediated Phosphorylation. The Journal of Biological Chemistry. 290: 27749-66. PMID 26391394 DOI: 10.1074/jbc.M115.683045  1
2015 Huang YM, Huber G, McCammon JA. Electrostatic steering enhances the rate of cAMP binding to phosphodiesterase: Brownian dynamics modeling. Protein Science : a Publication of the Protein Society. 24: 1884-9. PMID 26346301 DOI: 10.1002/pro.2794  0.88
2015 Kekenes-Huskey PM, Eun C, McCammon JA. Enzyme localization, crowding, and buffers collectively modulate diffusion-influenced signal transduction: Insights from continuum diffusion modeling. The Journal of Chemical Physics. 143: 094103. PMID 26342355 DOI: 10.1063/1.4929528  1
2015 Miao Y, Feher VA, McCammon JA. Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation. Journal of Chemical Theory and Computation. 11: 3584-3595. PMID 26300708 DOI: 10.1021/acs.jctc.5b00436  0.88
2015 Blachly PG, Sandala GM, Giammona DA, Bashford D, McCammon JA, Noodleman L. Broken-Symmetry DFT Computations for the Reaction Pathway of IspH, an Iron-Sulfur Enzyme in Pathogenic Bacteria. Inorganic Chemistry. 54: 6439-61. PMID 26098647 DOI: 10.1021/acs.inorgchem.5b00751  0.68
2015 Miao Y, Feixas F, Eun C, McCammon JA. Accelerated molecular dynamics simulations of protein folding. Journal of Computational Chemistry. 36: 1536-49. PMID 26096263 DOI: 10.1002/jcc.23964  0.88
2015 Kaus JW, Harder E, Lin T, Abel R, McCammon JA, Wang L. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations. Journal of Chemical Theory and Computation. 11: 2670-9. PMID 26085821 DOI: 10.1021/acs.jctc.5b00214  0.72
2015 Guo Z, Li B, Cheng LT, Zhou S, McCammon JA, Che J. Identification of protein-ligand binding sites by the level-set variational implicit-solvent approach. Journal of Chemical Theory and Computation. 11: 753-65. PMID 25941465 DOI: 10.1021/ct500867u  0.8
2015 Kaus JW, McCammon JA. Enhanced ligand sampling for relative protein-ligand binding free energy calculations. The Journal of Physical Chemistry. B. 119: 6190-7. PMID 25906170 DOI: 10.1021/acs.jpcb.5b02348  0.72
2015 Lindert S, McCammon JA. Improved cryoEM-Guided Iterative Molecular Dynamics--Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction. Journal of Chemical Theory and Computation. 11: 1337-46. PMID 25883538 DOI: 10.1021/ct500995d  0.76
2015 Miao Y, Caliman AD, McCammon JA. Allosteric effects of sodium ion binding on activation of the m3 muscarinic g-protein-coupled receptor. Biophysical Journal. 108: 1796-806. PMID 25863070 DOI: 10.1016/j.bpj.2015.03.003  0.88
2015 Kekenes-Huskey PM, Gillette AK, McCammon JA. Erratum: "Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation" [J. Chem. Phys. 140, 174106 (2014)]. The Journal of Chemical Physics. 142: 109902. PMID 25770569 DOI: 10.1063/1.4914327  0.92
2015 Zhou S, Cheng LT, Sun H, Che J, Dzubiella J, Li B, McCammon JA. LS-VISM: A software package for analysis of biomolecular solvation. Journal of Computational Chemistry. 36: 1047-59. PMID 25766844 DOI: 10.1002/jcc.23890  1
2015 Caliman AD, Swift SE, Wang Y, Miao Y, McCammon JA. Investigation of the conformational dynamics of the apo A2A adenosine receptor. Protein Science : a Publication of the Protein Society. 24: 1004-12. PMID 25761901 DOI: 10.1002/pro.2681  0.88
2015 Mouchlis VD, Bucher D, McCammon JA, Dennis EA. Membranes serve as allosteric activators of phospholipase A2, enabling it to extract, bind, and hydrolyze phospholipid substrates. Proceedings of the National Academy of Sciences of the United States of America. 112: E516-25. PMID 25624474 DOI: 10.1073/pnas.1424651112  0.4
2015 Lindert S, Cheng Y, Kekenes-Huskey P, Regnier M, McCammon JA. Effects of HCM cTnI mutation R145G on troponin structure and modulation by PKA phosphorylation elucidated by molecular dynamics simulations. Biophysical Journal. 108: 395-407. PMID 25606687 DOI: 10.1016/j.bpj.2014.11.3461  1
2015 Kim MO, Feng X, Feixas F, Zhu W, Lindert S, Bogue S, Sinko W, de Oliveira C, Rao G, Oldfield E, McCammon JA. A Molecular Dynamics Investigation of Mycobacterium tuberculosis Prenyl Synthases: Conformational Flexibility and Implications for Computer-aided Drug Discovery. Chemical Biology & Drug Design. 85: 756-69. PMID 25352216 DOI: 10.1111/cbdd.12463  1
2015 Lindert S, Tallorin L, Nguyen QG, Burkart MD, McCammon JA. In silico screening for Plasmodium falciparum enoyl-ACP reductase inhibitors. Journal of Computer-Aided Molecular Design. 29: 79-87. PMID 25344312 DOI: 10.1007/s10822-014-9806-3  0.76
2015 Kim MO, Blachly PG, Kaus JW, McCammon JA. Protocols utilizing constant pH molecular dynamics to compute pH-dependent binding free energies. The Journal of Physical Chemistry. B. 119: 861-72. PMID 25134690 DOI: 10.1021/jp505777n  0.72
2015 Lindert S, Li MX, Sykes BD, McCammon JA. Computer-aided drug discovery approach finds calcium sensitizer of cardiac troponin. Chemical Biology & Drug Design. 85: 99-106. PMID 24954187 DOI: 10.1111/cbdd.12381  0.76
2015 Sun H, Wen J, Zhao Y, Li B, Mccammon JA. A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics Journal of Chemical Physics. 143. DOI: 10.1063/1.4932336  1
2014 McCammon JA, Roux B, Voth G, Yang W. Special Issue on Free Energy. Journal of Chemical Theory and Computation. 10: 2631. PMID 26586502 DOI: 10.1021/ct500366u  0.96
2014 Wang N, Zhou S, Kekenes-Huskey PM, Li B, McCammon JA. Poisson-Boltzmann versus Size-Modified Poisson-Boltzmann Electrostatics Applied to Lipid Bilayers. The Journal of Physical Chemistry. B. 118: 14827-32. PMID 25426875 DOI: 10.1021/jp511702w  0.92
2014 Metzger VT, Eun C, Kekenes-Huskey PM, Huber G, McCammon JA. Electrostatic channeling in P. falciparum DHFR-TS: Brownian dynamics and Smoluchowski modeling. Biophysical Journal. 107: 2394-402. PMID 25418308 DOI: 10.1016/j.bpj.2014.09.039  0.92
2014 Cheng Y, Lindert S, Kekenes-Huskey P, Rao VS, Solaro RJ, Rosevear PR, Amaro R, McCulloch AD, McCammon JA, Regnier M. Computational studies of the effect of the S23D/S24D troponin I mutation on cardiac troponin structural dynamics. Biophysical Journal. 107: 1675-85. PMID 25296321 DOI: 10.1016/j.bpj.2014.08.008  1
2014 Tallorin L, Durrant JD, Nguyen QG, McCammon JA, Burkart MD. Celastrol inhibits Plasmodium falciparum enoyl-acyl carrier protein reductase. Bioorganic & Medicinal Chemistry. 22: 6053-61. PMID 25284249 DOI: 10.1016/j.bmc.2014.09.002  1
2014 Blachly PG, Sandala GM, Giammona DA, Liu T, Bashford D, McCammon JA, Noodleman L. Use of Broken-Symmetry Density Functional Theory To Characterize the IspH Oxidized State: Implications for IspH Mechanism and Inhibition. Journal of Chemical Theory and Computation. 10: 3871-3884. PMID 25221444 DOI: 10.1021/ct5005214  0.68
2014 Rao V, Cheng Y, Lindert S, Wang D, Oxenford L, McCulloch AD, McCammon JA, Regnier M. PKA phosphorylation of cardiac troponin I modulates activation and relaxation kinetics of ventricular myofibrils. Biophysical Journal. 107: 1196-204. PMID 25185555 DOI: 10.1016/j.bpj.2014.07.027  1
2014 Brown LM, Rogers KE, Aroonsakool N, McCammon JA, Insel PA. Allosteric inhibition of Epac: computational modeling and experimental validation to identify allosteric sites and inhibitors. The Journal of Biological Chemistry. 289: 29148-57. PMID 25183009 DOI: 10.1074/jbc.M114.569319  0.48
2014 Boechi L, Pierce L, Komives EA, McCammon JA. Trypsinogen activation as observed in accelerated molecular dynamics simulations. Protein Science : a Publication of the Protein Society. 23: 1550-8. PMID 25131668 DOI: 10.1002/pro.2532  0.56
2014 Martin DP, Blachly PG, McCammon JA, Cohen SM. Exploring the influence of the protein environment on metal-binding pharmacophores. Journal of Medicinal Chemistry. 57: 7126-35. PMID 25116076 DOI: 10.1021/jm500984b  0.68
2014 Miao Y, Sinko W, Pierce L, Bucher D, Walker RC, McCammon JA. Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation. Journal of Chemical Theory and Computation. 10: 2677-2689. PMID 25061441 DOI: 10.1021/ct500090q  0.88
2014 Liu YL, Lindert S, Zhu W, Wang K, McCammon JA, Oldfield E. Taxodione and arenarone inhibit farnesyl diphosphate synthase by binding to the isopentenyl diphosphate site. Proceedings of the National Academy of Sciences of the United States of America. 111: E2530-9. PMID 24927548 DOI: 10.1073/pnas.1409061111  0.8
2014 Eun C, Ortiz-Sánchez JM, Da L, Wang D, McCammon JA. Molecular dynamics simulation study of conformational changes of transcription factor TFIIS during RNA polymerase II transcriptional arrest and reactivation. Plos One. 9: e97975. PMID 24842057 DOI: 10.1371/journal.pone.0097975  0.72
2014 Sinko W, Wang Y, Zhu W, Zhang Y, Feixas F, Cox CL, Mitchell DA, Oldfield E, McCammon JA. Undecaprenyl diphosphate synthase inhibitors: antibacterial drug leads. Journal of Medicinal Chemistry. 57: 5693-701. PMID 24827744 DOI: 10.1021/jm5004649  1
2014 Kekenes-Huskey PM, Gillette AK, McCammon JA. Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation. The Journal of Chemical Physics. 140: 174106. PMID 24811624 DOI: 10.1063/1.4873382  1
2014 Götz AW, Bucher D, Lindert S, McCammon JA. Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields. Journal of Chemical Theory and Computation. 10: 1631-1637. PMID 24803868 DOI: 10.1021/ct401049q  0.76
2014 Zhou S, Cheng LT, Dzubiella J, Li B, McCammon JA. Variational Implicit Solvation with Poisson-Boltzmann Theory. Journal of Chemical Theory and Computation. 10: 1454-1467. PMID 24803864 DOI: 10.1021/ct401058w  1
2014 Guo Z, Li B, Dzubiella J, Cheng LT, McCammon JA, Che J. Heterogeneous Hydration of p53/MDM2 Complex. Journal of Chemical Theory and Computation. 10: 1302-1313. PMID 24803860 DOI: 10.1021/ct400967m  1
2014 Kaus JW, Arrar M, McCammon JA. Accelerated adaptive integration method. The Journal of Physical Chemistry. B. 118: 5109-18. PMID 24780083 DOI: 10.1021/jp502358y  0.76
2014 Martin DP, Blachly PG, Marts AR, Woodruff TM, de Oliveira CA, McCammon JA, Tierney DL, Cohen SM. 'Unconventional' coordination chemistry by metal chelating fragments in a metalloprotein active site. Journal of the American Chemical Society. 136: 5400-6. PMID 24635441 DOI: 10.1021/ja500616m  0.76
2014 Eun C, Kekenes-Huskey PM, Metzger VT, McCammon JA. A model study of sequential enzyme reactions and electrostatic channeling. The Journal of Chemical Physics. 140: 105101. PMID 24628210 DOI: 10.1063/1.4867286  0.92
2014 Lindert S, Maslennikov I, Chiu EJ, Pierce LC, McCammon JA, Choe S. Drug screening strategy for human membrane proteins: from NMR protein backbone structure to in silica- and NMR-screened hits. Biochemical and Biophysical Research Communications. 445: 724-33. PMID 24525125 DOI: 10.1016/j.bbrc.2014.01.179  0.76
2014 Jacobitz AW, Wereszczynski J, Yi SW, Amer BR, Huang GL, Nguyen AV, Sawaya MR, Jung ME, McCammon JA, Clubb RT. Structural and computational studies of the Staphylococcus aureus sortase B-substrate complex reveal a substrate-stabilized oxyanion hole. The Journal of Biological Chemistry. 289: 8891-902. PMID 24519933 DOI: 10.1074/jbc.M113.509273  0.32
2014 Brown LM, Rogers KE, McCammon JA, Insel PA. Identification and validation of modulators of exchange protein activated by cAMP (Epac) activity: structure-function implications for Epac activation and inhibition. The Journal of Biological Chemistry. 289: 8217-30. PMID 24497631 DOI: 10.1074/jbc.M114.548636  0.48
2014 Miao Y, Nichols SE, McCammon JA. Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics. Physical Chemistry Chemical Physics : Pccp. 16: 6398-406. PMID 24445284 DOI: 10.1039/c3cp53962h  0.88
2014 Ivetac A, Swift SE, Boyer PL, Diaz A, Naughton J, Young JA, Hughes SH, McCammon JA. Discovery of novel inhibitors of HIV-1 reverse transcriptase through virtual screening of experimental and theoretical ensembles. Chemical Biology & Drug Design. 83: 521-31. PMID 24405985 DOI: 10.1111/cbdd.12277  0.36
2014 Miller B, Friedman AJ, Choi H, Hogan J, McCammon JA, Hook V, Gerwick WH. The marine cyanobacterial metabolite gallinamide A is a potent and selective inhibitor of human cathepsin L. Journal of Natural Products. 77: 92-9. PMID 24364476 DOI: 10.1021/np400727r  0.48
2014 Nguyen C, Haushalter RW, Lee DJ, Markwick PR, Bruegger J, Caldara-Festin G, Finzel K, Jackson DR, Ishikawa F, O'Dowd B, McCammon JA, Opella SJ, Tsai SC, Burkart MD. Trapping the dynamic acyl carrier protein in fatty acid biosynthesis. Nature. 505: 427-31. PMID 24362570 DOI: 10.1038/nature12810  0.56
2014 Feixas F, Lindert S, Sinko W, McCammon JA. Exploring the role of receptor flexibility in structure-based drug discovery. Biophysical Chemistry. 186: 31-45. PMID 24332165 DOI: 10.1016/j.bpc.2013.10.007  0.76
2014 Miao Y, Nichols SE, McCammon JA. Mapping of allosteric druggable sites in activation-associated conformers of the M2 muscarinic receptor. Chemical Biology & Drug Design. 83: 237-46. PMID 24112716 DOI: 10.1111/cbdd.12233  0.88
2014 Kim MO, Feixas-Gerones F, Oldfield E, McCammon JA. A Molecular Dynamics Investigation of the Bacterial Cis-Prenyl Transferases: Perspectives on Conformational Flexibility and Chain Elongation Mechanisms Biophysical Journal. 106: 659a. DOI: 10.1016/j.bpj.2013.11.3649  0.8
2013 Lindert S, Bucher D, Eastman P, Pande V, McCammon JA. Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units. Journal of Chemical Theory and Computation. 9: 4684-4691. PMID 24634618 DOI: 10.1021/ct400514p  0.76
2013 Blachly PG, de Oliveira CA, Williams SL, McCammon JA. Utilizing a dynamical description of IspH to aid in the development of novel antimicrobial drugs. Plos Computational Biology. 9: e1003395. PMID 24367248 DOI: 10.1371/journal.pcbi.1003395  0.76
2013 Liao T, Zhang Y, Kekenes-Huskey PM, Cheng Y, Michailova A, McCulloch AD, Holst M, McCammon JA. Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes. Molecular Based Mathematical Biology (Online). 1. PMID 24352481 DOI: 10.2478/mlbmb-2013-0009  1
2013 Kekenes-Huskey PM, Liao T, Gillette AK, Hake JE, Zhang Y, Michailova AP, McCulloch AD, McCammon JA. Molecular and subcellular-scale modeling of nucleotide diffusion in the cardiac myofilament lattice. Biophysical Journal. 105: 2130-40. PMID 24209858 DOI: 10.1016/j.bpj.2013.09.020  1
2013 Kaus JW, Pierce LT, Walker RC, McCammont JA. Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package. Journal of Chemical Theory and Computation. 9. PMID 24185531 DOI: 10.1021/ct400340s  1
2013 Zhou S, Rogers KE, de Oliveira CA, Baron R, Cheng LT, Dzubiella J, Li B, McCammon JA. Variational Implicit-Solvent Modeling of Host-Guest Binding: A Case Study on Cucurbit[7]uril| Journal of Chemical Theory and Computation. 9: 4195-4204. PMID 24039554 DOI: 10.1021/ct400232m  1
2013 Lindert S, Meiler J, McCammon JA. Iterative Molecular Dynamics-Rosetta Protein Structure Refinement Protocol to Improve Model Quality. Journal of Chemical Theory and Computation. 9: 3843-3847. PMID 23956701 DOI: 10.1021/ct400260c  0.76
2013 Bucher D, Hsu YH, Mouchlis VD, Dennis EA, McCammon JA. Insertion of the Ca²⁺-independent phospholipase A₂ into a phospholipid bilayer via coarse-grained and atomistic molecular dynamics simulations. Plos Computational Biology. 9: e1003156. PMID 23935474 DOI: 10.1371/journal.pcbi.1003156  0.4
2013 Boechi L, de Oliveira CA, Da Fonseca I, Kizjakina K, Sobrado P, Tanner JJ, McCammon JA. Substrate-dependent dynamics of UDP-galactopyranose mutase: Implications for drug design. Protein Science : a Publication of the Protein Society. 22: 1490-501. PMID 23934860 DOI: 10.1002/pro.2332  0.76
2013 Arrar M, de Oliveira CA, McCammon JA. Inactivating mutation in histone deacetylase 3 stabilizes its active conformation. Protein Science : a Publication of the Protein Society. 22: 1306-12. PMID 23904210 DOI: 10.1002/pro.2317  0.76
2013 Eun C, Kekenes-Huskey PM, McCammon JA. Influence of neighboring reactive particles on diffusion-limited reactions. The Journal of Chemical Physics. 139: 044117. PMID 23901970 DOI: 10.1063/1.4816522  0.92
2013 Tikhonova IG, Selvam B, Ivetac A, Wereszczynski J, McCammon JA. Simulations of biased agonists in the β(2) adrenergic receptor with accelerated molecular dynamics. Biochemistry. 52: 5593-603. PMID 23879802 DOI: 10.1021/bi400499n  0.32
2013 Zhao Y, Kwan YY, Che J, Li B, McCammon JA. Phase-field approach to implicit solvation of biomolecules with Coulomb-field approximation. The Journal of Chemical Physics. 139: 024111. PMID 23862933 DOI: 10.1063/1.4812839  0.8
2013 Durrant JD, Lindert S, McCammon JA. AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design. Journal of Molecular Graphics & Modelling. 44: 104-12. PMID 23792207 DOI: 10.1016/j.jmgm.2013.05.006  1
2013 Miao Y, Nichols SE, Gasper PM, Metzger VT, McCammon JA. Activation and dynamic network of the M2 muscarinic receptor. Proceedings of the National Academy of Sciences of the United States of America. 110: 10982-7. PMID 23781107 DOI: 10.1073/pnas.1309755110  0.88
2013 Wang N, Huber GA, McCammon JA. Assessing the two-body diffusion tensor calculated by the bead models. The Journal of Chemical Physics. 138: 204117. PMID 23742464 DOI: 10.1063/1.4807590  0.88
2013 Durrant JD, Friedman AJ, Rogers KE, McCammon JA. Comparing neural-network scoring functions and the state of the art: applications to common library screening. Journal of Chemical Information and Modeling. 53: 1726-35. PMID 23734946 DOI: 10.1021/ci400042y  1
2013 Sinko W, Miao Y, de Oliveira CA, McCammon JA. Population based reweighting of scaled molecular dynamics. The Journal of Physical Chemistry. B. 117: 12759-68. PMID 23721224 DOI: 10.1021/jp401587e  0.88
2013 Chan AH, Wereszczynski J, Amer BR, Yi SW, Jung ME, McCammon JA, Clubb RT. Discovery of Staphylococcus aureus sortase A inhibitors using virtual screening and the relaxed complex scheme. Chemical Biology & Drug Design. 82: 418-28. PMID 23701677 DOI: 10.1111/cbdd.12167  0.32
2013 Fuglestad B, Gasper PM, McCammon JA, Markwick PR, Komives EA. Correlated motions and residual frustration in thrombin. The Journal of Physical Chemistry. B. 117: 12857-63. PMID 23621631 DOI: 10.1021/jp402107u  0.72
2013 Kim MO, Nichols SE, Wang Y, McCammon JA. Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC. Journal of Computer-Aided Molecular Design. 27: 235-46. PMID 23579613 DOI: 10.1007/s10822-013-9643-9  0.8
2013 Nichols SE, Hernández CX, Wang Y, McCammon JA. Structure-based network analysis of an evolved G protein-coupled receptor homodimer interface. Protein Science : a Publication of the Protein Society. 22: 745-54. PMID 23553730 DOI: 10.1002/pro.2258  1
2013 Guo Z, Li B, Dzubiella J, Cheng LT, McCammon JA, Che J. Evaluation of Hydration Free Energy by Level-Set Variational Implicit-Solvent Model with Coulomb-Field Approximation. Journal of Chemical Theory and Computation. 9: 1778-1787. PMID 23505345 DOI: 10.1021/ct301087w  1
2013 Baron R, McCammon JA. Molecular recognition and ligand association. Annual Review of Physical Chemistry. 64: 151-75. PMID 23473376 DOI: 10.1146/annurev-physchem-040412-110047  0.76
2013 Lindert S, Zhu W, Liu YL, Pang R, Oldfield E, McCammon JA. Farnesyl diphosphate synthase inhibitors from in silico screening. Chemical Biology & Drug Design. 81: 742-8. PMID 23421555 DOI: 10.1111/cbdd.12121  0.8
2013 Rogers KE, Ortiz-Sánchez JM, Baron R, Fajer M, de Oliveira CA, McCammon JA. On the Role of Dewetting Transitions in Host-Guest Binding Free Energy Calculations. Journal of Chemical Theory and Computation. 9: 46-53. PMID 23316123 DOI: 10.1021/ct300515n  1
2013 Arrar M, de Oliveira CA, Fajer M, Sinko W, McCammon JA. w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations. Journal of Chemical Theory and Computation. 9: 18-23. PMID 23316122 DOI: 10.1021/ct300896h  1
2013 Setny P, Baron R, Michael Kekenes-Huskey P, McCammon JA, Dzubiella J. Solvent fluctuations in hydrophobic cavity-ligand binding kinetics. Proceedings of the National Academy of Sciences of the United States of America. 110: 1197-202. PMID 23297241 DOI: 10.1073/pnas.1221231110  1
2013 Hsu YH, Bucher D, Cao J, Li S, Yang SW, Kokotos G, Woods VL, McCammon JA, Dennis EA. Fluoroketone inhibition of Ca(2+)-independent phospholipase A2 through binding pocket association defined by hydrogen/deuterium exchange and molecular dynamics. Journal of the American Chemical Society. 135: 1330-7. PMID 23256506 DOI: 10.1021/ja306490g  0.4
2013 Sinko W, Lindert S, McCammon JA. Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design. Chemical Biology & Drug Design. 81: 41-9. PMID 23253130 DOI: 10.1111/cbdd.12051  0.76
2013 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, ... ... McCammon JA, et al. Antibacterial drug leads targeting isoprenoid biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 110: 123-8. PMID 23248302 DOI: 10.1073/pnas.1219899110  1
2013 Arrar M, Turnham R, Pierce L, de Oliveira CA, McCammon JA. Structural insight into the separate roles of inositol tetraphosphate and deacetylase-activating domain in activation of histone deacetylase 3. Protein Science : a Publication of the Protein Society. 22: 83-92. PMID 23139175 DOI: 10.1002/pro.2190  0.76
2013 Zhang B, Lu B, Cheng X, Huang J, Pitsianis NP, Sun X, McCammon JA. Mathematical and numerical aspects of the adaptive fast multipole Poisson-Boltzmann solver Communications in Computational Physics. 13: 107-128. DOI: 10.4208/cicp.210711.111111s  1
2013 Setny P, Baron R, McCammon JA. Comment on 'Molecular driving forces of the pocket-ligand hydrophobic association' by G. Graziano, Chem. Phys. Lett. 533 (2012) 95 Chemical Physics Letters. 555: 306-309. DOI: 10.1016/j.cplett.2012.11.004  1
2013 Lu B, Cheng X, Huang J, McCammon JA. AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems Computer Physics Communications. 184: 2618-2619. DOI: 10.1016/j.cpc.2013.05.012  1
2012 Kekenes-Huskey PM, Gillette A, Hake J, McCammon JA. Finite Element Estimation of Protein-Ligand Association Rates with Post-Encounter Effects: Applications to Calcium binding in Troponin C and SERCA. Computational Science & Discovery. 5. PMID 23293662 DOI: 10.1088/1749-4699/5/1/014015  1
2012 Kekenes-Huskey PM, Lindert S, McCammon JA. Molecular basis of calcium-sensitizing and desensitizing mutations of the human cardiac troponin C regulatory domain: a multi-scale simulation study. Plos Computational Biology. 8: e1002777. PMID 23209387 DOI: 10.1371/journal.pcbi.1002777  1
2012 Gasper PM, Fuglestad B, Komives EA, Markwick PR, McCammon JA. Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities. Proceedings of the National Academy of Sciences of the United States of America. 109: 21216-22. PMID 23197839 DOI: 10.1073/pnas.1218414109  0.72
2012 Lindert S, Kekenes-Huskey PM, McCammon JA. Long-timescale molecular dynamics simulations elucidate the dynamics and kinetics of exposure of the hydrophobic patch in troponin C. Biophysical Journal. 103: 1784-9. PMID 23083722 DOI: 10.1016/j.bpj.2012.08.058  0.92
2012 Kekenes-Huskey PM, Cheng Y, Hake JE, Sachse FB, Bridge JH, Holst MJ, McCammon JA, McCulloch AD, Michailova AP. Modeling effects of L-type ca(2+) current and na(+)-ca(2+) exchanger on ca(2+) trigger flux in rabbit myocytes with realistic T-tubule geometries. Frontiers in Physiology. 3: 351. PMID 23060801 DOI: 10.3389/fphys.2012.00351  1
2012 Kappel K, Wereszczynski J, Clubb RT, McCammon JA. The binding mechanism, multiple binding modes, and allosteric regulation of Staphylococcus aureus Sortase A probed by molecular dynamics simulations. Protein Science : a Publication of the Protein Society. 21: 1858-71. PMID 23023444 DOI: 10.1002/pro.2168  0.32
2012 Pierce LC, Salomon-Ferrer R, Augusto F de Oliveira C, McCammon JA, Walker RC. Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics. Journal of Chemical Theory and Computation. 8: 2997-3002. PMID 22984356 DOI: 10.1021/ct300284c  0.64
2012 Lindert S, McCammon JA. Dynamics of Plasmodium falciparum enoyl-ACP reductase and implications on drug discovery. Protein Science : a Publication of the Protein Society. 21: 1734-45. PMID 22969045 DOI: 10.1002/pro.2155  0.76
2012 Konecny R, Baker NA, McCammon JA. iAPBS: a programming interface to Adaptive Poisson-Boltzmann Solver (APBS). Computational Science & Discovery. 5. PMID 22905037 DOI: 10.1088/1749-4699/5/1/015005  0.96
2012 Ortiz-Sánchez JM, Bucher D, Pierce LC, Markwick PR, McCammon JA. Exploring the Photophysical Properties of Molecular Systems Using Excited State Accelerated ab Initio Molecular Dynamics. Journal of Chemical Theory and Computation. 8: 2752-2761. PMID 22904696 DOI: 10.1021/ct200740r  0.56
2012 Schlamadinger DE, Wang Y, McCammon JA, Kim JE. Spectroscopic and computational study of melittin, cecropin A, and the hybrid peptide CM15. The Journal of Physical Chemistry. B. 116: 10600-8. PMID 22845179 DOI: 10.1021/jp304021t  0.8
2012 Fuglestad B, Gasper PM, Tonelli M, McCammon JA, Markwick PR, Komives EA. The dynamic structure of thrombin in solution. Biophysical Journal. 103: 79-88. PMID 22828334 DOI: 10.1016/j.bpj.2012.05.047  0.72
2012 Kekenes-Huskey PM, Metzger VT, Grant BJ, Andrew McCammon J. Calcium binding and allosteric signaling mechanisms for the sarcoplasmic reticulum Ca²+ ATPase. Protein Science : a Publication of the Protein Society. 21: 1429-43. PMID 22821874 DOI: 10.1002/pro.2129  1
2012 Ortiz-Sanchez JM, Nichols SE, Sayyah J, Brown JH, McCammon JA, Grant BJ. Identification of potential small molecule binding pockets on Rho family GTPases. Plos One. 7: e40809. PMID 22815826 DOI: 10.1371/journal.pone.0040809  0.76
2012 Rogers KE, Keränen H, Durrant JD, Ratnam J, Doak A, Arkin MR, McCammon JA. Novel cruzain inhibitors for the treatment of Chagas' disease. Chemical Biology & Drug Design. 80: 398-405. PMID 22613098 DOI: 10.1111/j.1747-0285.2012.01416.x  1
2012 Lindert S, Durrant JD, McCammon JA. LigMerge: a fast algorithm to generate models of novel potential ligands from sets of known binders. Chemical Biology & Drug Design. 80: 358-65. PMID 22594624 DOI: 10.1111/j.1747-0285.2012.01414.x  1
2012 Salmon L, Pierce L, Grimm A, Ortega Roldan JL, Mollica L, Jensen MR, van Nuland N, Markwick PR, McCammon JA, Blackledge M. Multi-timescale conformational dynamics of the SH3 domain of CD2-associated protein using NMR spectroscopy and accelerated molecular dynamics. Angewandte Chemie (International Ed. in English). 51: 6103-6. PMID 22565613 DOI: 10.1002/anie.201202026  0.56
2012 Bauler P, Huber GA, McCammon JA. Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions. The Journal of Chemical Physics. 136: 164107. PMID 22559470 DOI: 10.1063/1.4704808  0.6
2012 Wereszczynski J, McCammon JA. Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations. Proceedings of the National Academy of Sciences of the United States of America. 109: 7759-64. PMID 22547793 DOI: 10.1073/pnas.1117441109  0.32
2012 Hake J, Edwards AG, Yu Z, Kekenes-Huskey PM, Michailova AP, McCammon JA, Holst MJ, Hoshijima M, McCulloch AD. Modelling cardiac calcium sparks in a three-dimensional reconstruction of a calcium release unit. The Journal of Physiology. 590: 4403-22. PMID 22495592 DOI: 10.1113/jphysiol.2012.227926  0.92
2012 Friedman AJ, Durrant JD, Pierce LC, McCorvie TJ, Timson DJ, McCammon JA. The molecular dynamics of Trypanosoma brucei UDP-galactose 4'-epimerase: a drug target for African sleeping sickness. Chemical Biology & Drug Design. 80: 173-81. PMID 22487100 DOI: 10.1111/j.1747-0285.2012.01392.x  1
2012 Durrant JD, McCammon JA. AutoClickChem: click chemistry in silico. Plos Computational Biology. 8: e1002397. PMID 22438795 DOI: 10.1371/journal.pcbi.1002397  1
2012 Wang Y, Schlamadinger DE, Kim JE, McCammon JA. Comparative molecular dynamics simulations of the antimicrobial peptide CM15 in model lipid bilayers. Biochimica Et Biophysica Acta. 1818: 1402-9. PMID 22387432 DOI: 10.1016/j.bbamem.2012.02.017  0.8
2012 Lawrenz M, Wereszczynski J, Ortiz-Sánchez JM, Nichols SE, McCammon JA. Thermodynamic integration to predict host-guest binding affinities. Journal of Computer-Aided Molecular Design. 26: 569-76. PMID 22350568 DOI: 10.1007/s10822-012-9542-5  0.72
2012 Wang Z, Che J, Cheng LT, Dzubiella J, Li B, McCammon JA. Level-Set Variational Implicit-Solvent Modeling of Biomolecules with the Coulomb-Field Approximation. Journal of Chemical Theory and Computation. 8: 386-397. PMID 22346739 DOI: 10.1021/ct200647j  1
2012 Lindert S, Kekenes-Huskey PM, Huber G, Pierce L, McCammon JA. Dynamics and calcium association to the N-terminal regulatory domain of human cardiac troponin C: a multiscale computational study. The Journal of Physical Chemistry. B. 116: 8449-59. PMID 22329450 DOI: 10.1021/jp212173f  0.92
2012 Sinko W, de Oliveira CA, Pierce LC, McCammon JA. Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 8: 17-23. PMID 22241967 DOI: 10.1021/ct200615k  0.76
2012 Wereszczynski J, McCammon JA. Simulations of the p97 complex suggest novel conformational states of hydrolysis intermediates. Protein Science : a Publication of the Protein Society. 21: 475-86. PMID 22238181 DOI: 10.1002/pro.2024  0.32
2012 Sinko W, Sierecki E, de Oliveira CA, McCammon JA. Guide to virtual screening: application to the Akt phosphatase PHLPP. Methods in Molecular Biology (Clifton, N.J.). 819: 561-73. PMID 22183558 DOI: 10.1007/978-1-61779-465-0_33  0.76
2012 Wereszczynski J, McCammon JA. Accelerated molecular dynamics in computational drug design. Methods in Molecular Biology (Clifton, N.J.). 819: 515-24. PMID 22183555 DOI: 10.1007/978-1-61779-465-0_30  0.32
2012 Lawrenz M, Baron R, Wang Y, McCammon JA. Independent-Trajectory Thermodynamic Integration: a practical guide to protein-drug binding free energy calculations using distributed computing. Methods in Molecular Biology (Clifton, N.J.). 819: 469-86. PMID 22183552 DOI: 10.1007/978-1-61779-465-0_27  0.8
2012 Nichols SE, Baron R, McCammon JA. On the use of molecular dynamics receptor conformations for virtual screening. Methods in Molecular Biology (Clifton, N.J.). 819: 93-103. PMID 22183532 DOI: 10.1007/978-1-61779-465-0_7  0.76
2012 Wereszczynski J, McCammon JA. Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition. Quarterly Reviews of Biophysics. 45: 1-25. PMID 22082669 DOI: 10.1017/S0033583511000096  0.32
2012 Holst M, McCammon JA, Yu Z, Zhou Y, Zhu Y. ADAPTIVE FINITE ELEMENT MODELING TECHNIQUES FOR THE POISSON-BOLTZMANN EQUATION. Communications in Computational Physics. 11: 179-214. PMID 21949541 DOI: 10.4208/cicp.081009.130611a  1
2012 Cheng Y, Kekenes-Huskey P, Hake E, Holst J, McCammon A, Michailova P, Hake JE, Holst MJ, McCammon JA, Michailova AP. Multi-scale continuum modeling of biological processes: From molecular electro-diffusion to sub-cellular signaling transduction Computational Science and Discovery. 5. DOI: 10.1088/1749-4699/5/1/015002  1
2012 McCammon JA. Chapter 13: Computer-aided drug discovery: Two antiviral drugs for HIV/AIDS Rsc Biomolecular Sciences. 316-319.  1
2011 Grant BJ, Gheorghe DM, Zheng W, Alonso M, Huber G, Dlugosz M, McCammon JA, Cross RA. Electrostatically biased binding of kinesin to microtubules. Plos Biology. 9: e1001207. PMID 22140358 DOI: 10.1371/journal.pbio.1001207  0.76
2011 Williams SL, Blachly PG, McCammon JA. Measuring the successes and deficiencies of constant pH molecular dynamics: a blind prediction study. Proteins. 79: 3381-8. PMID 22072520 DOI: 10.1002/prot.23136  0.68
2011 Bucher D, Grant BJ, McCammon JA. Induced fit or conformational selection? The role of the semi-closed state in the maltose binding protein. Biochemistry. 50: 10530-9. PMID 22050600 DOI: 10.1021/bi201481a  0.76
2011 Grant BJ, Lukman S, Hocker HJ, Sayyah J, Brown JH, McCammon JA, Gorfe AA. Novel allosteric sites on Ras for lead generation. Plos One. 6: e25711. PMID 22046245 DOI: 10.1371/journal.pone.0025711  0.76
2011 Durrant JD, McCammon JA. Molecular dynamics simulations and drug discovery. Bmc Biology. 9: 71. PMID 22035460 DOI: 10.1186/1741-7007-9-71  1
2011 de Oliveira CA, Grant BJ, Zhou M, McCammon JA. Large-scale conformational changes of Trypanosoma cruzi proline racemase predicted by accelerated molecular dynamics simulation. Plos Computational Biology. 7: e1002178. PMID 22022240 DOI: 10.1371/journal.pcbi.1002178  0.76
2011 Durrant JD, McCammon JA. NNScore 2.0: a neural-network receptor-ligand scoring function. Journal of Chemical Information and Modeling. 51: 2897-903. PMID 22017367 DOI: 10.1021/ci2003889  1
2011 Markwick PR, McCammon JA. Studying functional dynamics in bio-molecules using accelerated molecular dynamics. Physical Chemistry Chemical Physics : Pccp. 13: 20053-65. PMID 22015376 DOI: 10.1039/c1cp22100k  0.56
2011 Wang Y, Markwick PR, de Oliveira CA, McCammon JA. Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics. Journal of Chemical Theory and Computation. 7: 3199-3207. PMID 22003320 DOI: 10.1021/ct200430c  0.8
2011 Durrant JD, Friedman AJ, McCammon JA. CrystalDock: a novel approach to fragment-based drug design. Journal of Chemical Information and Modeling. 51: 2573-80. PMID 21910501 DOI: 10.1021/ci200357y  1
2011 Durrant JD, McCammon JA. HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis. Journal of Molecular Graphics & Modelling. 31: 5-9. PMID 21880522 DOI: 10.1016/j.jmgm.2011.07.008  1
2011 Durrant JD, McCammon JA. Towards the development of novel Trypanosoma brucei RNA editing ligase 1 inhibitors. Bmc Pharmacology. 11: 9. PMID 21878090 DOI: 10.1186/1471-2210-11-9  1
2011 Romanowska J, McCammon JA, Trylska J. Understanding the origins of bacterial resistance to aminoglycosides through molecular dynamics mutational study of the ribosomal A-site. Plos Computational Biology. 7: e1002099. PMID 21814503 DOI: 10.1371/journal.pcbi.1002099  0.56
2011 Lawrenz M, Baron R, Wang Y, McCammon JA. Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies. Journal of Chemical Theory and Computation. 7: 2224-2232. PMID 21811708 DOI: 10.1021/ct200230v  0.8
2011 Durrant JD, Cao R, Gorfe AA, Zhu W, Li J, Sankovsky A, Oldfield E, McCammon JA. Non-bisphosphonate inhibitors of isoprenoid biosynthesis identified via computer-aided drug design. Chemical Biology & Drug Design. 78: 323-32. PMID 21696546 DOI: 10.1111/j.1747-0285.2011.01164.x  1
2011 Wang Y, Harrison CB, Schulten K, McCammon JA. Implementation of Accelerated Molecular Dynamics in NAMD. Computational Science & Discovery. 4. PMID 21686063 DOI: 10.1088/1749-4699/4/1/015002  0.8
2011 Ivetac A, McCammon JA. Molecular recognition in the case of flexible targets. Current Pharmaceutical Design. 17: 1663-71. PMID 21619526 DOI: 10.2174/138161211796355056  1
2011 Durrant JD, de Oliveira CA, McCammon JA. Pyrone-based inhibitors of metalloproteinase types 2 and 3 may work as conformation-selective inhibitors. Chemical Biology & Drug Design. 78: 191-8. PMID 21609408 DOI: 10.1111/j.1747-0285.2011.01148.x  1
2011 McCammon JA. Gated Diffusion-controlled Reactions. Bmc Biophysics. 4: 4. PMID 21595999 DOI: 10.1186/2046-1682-4-4  1
2011 Mereghetti P, Kokh D, McCammon JA, Wade RC. Diffusion and association processes in biological systems: theory, computation and experiment. Bmc Biophysics. 4: 2. PMID 21595997 DOI: 10.1186/2046-1682-4-2  1
2011 Pierce LC, Markwick PR, McCammon JA, Doltsinis NL. Accelerating chemical reactions: exploring reactive free-energy surfaces using accelerated ab initio molecular dynamics. The Journal of Chemical Physics. 134: 174107. PMID 21548673 DOI: 10.1063/1.3581093  1
2011 Nichols SE, Baron R, Ivetac A, McCammon JA. Predictive power of molecular dynamics receptor structures in virtual screening. Journal of Chemical Information and Modeling. 51: 1439-46. PMID 21534609 DOI: 10.1021/ci200117n  1
2011 Bucher D, Grant BJ, Markwick PR, McCammon JA. Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics. Plos Computational Biology. 7: e1002034. PMID 21533070 DOI: 10.1371/journal.pcbi.1002034  1
2011 Bucher D, Pierce LC, McCammon JA, Markwick PR. On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations. Journal of Chemical Theory and Computation. 7: 890-897. PMID 21494425 DOI: 10.1021/ct100605v  1
2011 Skjaerven L, Grant B, Muga A, Teigen K, McCammon JA, Reuter N, Martinez A. Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations Plos Computational Biology. 7. PMID 21423709 DOI: 10.1371/journal.pcbi.1002004  1
2011 Długosz M, Huber GA, McCammon JA, Trylska J. Brownian dynamics study of the association between the 70S ribosome and elongation factor G Biopolymers. 95: 616-627. PMID 21394717 DOI: 10.1002/bip.21619  1
2011 Sander T, Frølund B, Bruun AT, Ivanov I, Mccammon JA, Balle T. New insights into the GABA A receptor structure and orthosteric ligand binding: Receptor modeling guided by experimental data Proteins: Structure, Function and Bioinformatics. 79: 1458-1477. PMID 21365676 DOI: 10.1002/prot.22975  1
2011 Durrant JD, McCammon JA. BINANA: a novel algorithm for ligand-binding characterization. Journal of Molecular Graphics & Modelling. 29: 888-93. PMID 21310640 DOI: 10.1016/j.jmgm.2011.01.004  1
2011 Baron R, Binda C, Tortorici M, McCammon JA, Mattevi A. Molecular mimicry and ligand recognition in binding and catalysis by the histone demethylase LSD1-CoREST complex Structure. 19: 212-220. PMID 21300290 DOI: 10.1016/j.str.2011.01.001  1
2011 Sinko W, de Oliveira C, Williams S, Van Wynsberghe A, Durrant JD, Cao R, Oldfield E, McCammon JA. Applying molecular dynamics simulations to identify rarely sampled ligand-bound conformational states of undecaprenyl pyrophosphate synthase, an antibacterial target. Chemical Biology & Drug Design. 77: 412-20. PMID 21294851 DOI: 10.1111/j.1747-0285.2011.01101.x  1
2011 Williams SL, de Oliveira CA, Vazquez H, McCammon JA. From Zn to Mn: the study of novel manganese-binding groups in the search for new drugs against tuberculosis. Chemical Biology & Drug Design. 77: 117-23. PMID 21266015 DOI: 10.1111/j.1747-0285.2010.01060.x  1
2011 Durrant JD, de Oliveira CA, McCammon JA. POVME: an algorithm for measuring binding-pocket volumes. Journal of Molecular Graphics & Modelling. 29: 773-6. PMID 21147010 DOI: 10.1016/j.jmgm.2010.10.007  1
2011 Radford RJ, Lawrenz M, Nguyen PC, McCammon JA, Tezcan FA. Porous protein frameworks with unsaturated metal centers in sterically encumbered coordination sites. Chemical Communications (Cambridge, England). 47: 313-5. PMID 20740227 DOI: 10.1039/c0cc02168g  1
2011 Markwick PRL, Pierce LCT, Goodin DB, McCammon JA. Adaptive accelerated molecular dynamics (Ad-AMD) revealing the molecular plasticity of P450cam Journal of Physical Chemistry Letters. 2: 158-164. DOI: 10.1021/jz101462n  1
2010 Lu B, Holst MJ, McCammon JA, Zhou YC. Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions. Journal of Computational Physics. 229: 6979-6994. PMID 21709855 DOI: 10.1016/j.jcp.2010.05.035  0.84
2010 Grant BJ, McCammon JA, Gorfe AA. Conformational selection in G-proteins: Lessons from Ras and Rho Biophysical Journal. 99: L87-L89. PMID 21112273 DOI: 10.1016/j.bpj.2010.10.020  1
2010 Cheng Y, Yu Z, Hoshijima M, Holst MJ, McCulloch AD, McCammon JA, Michailova AP. Numerical analysis of Ca2+ signaling in rat ventricular myocytes with realistic transverse-axial tubular geometry and inhibited sarcoplasmic reticulum. Plos Computational Biology. 6: e1000972. PMID 21060856 DOI: 10.1371/journal.pcbi.1000972  1
2010 Durrant JD, McCammon JA. Computer-aided drug-discovery techniques that account for receptor flexibility. Current Opinion in Pharmacology. 10: 770-4. PMID 20888294 DOI: 10.1016/j.coph.2010.09.001  1
2010 Durrant JD, McCammon JA. NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexes. Journal of Chemical Information and Modeling. 50: 1865-71. PMID 20845954 DOI: 10.1021/ci100244v  1
2010 Lukman S, Grant BJ, Gorfe AA, Grant GH, McCammon JA. The distinct conformational dynamics of K-Ras and H-Ras A59G. Plos Computational Biology. 6. PMID 20838576 DOI: 10.1371/journal.pcbi.1000922  1
2010 Sierecki E, Sinko W, McCammon JA, Newton AC. Discovery of small molecule inhibitors of the PH domain leucine-rich repeat protein phosphatase (PHLPP) by chemical and virtual screening. Journal of Medicinal Chemistry. 53: 6899-911. PMID 20836557 DOI: 10.1021/jm100331d  0.76
2010 Ishizuka R, Huber GA, McCammon JA. Solvation Effect on the Conformations of Alanine Dipeptide: Integral Equation Approach. The Journal of Physical Chemistry Letters. 1: 2279-2283. PMID 20694049 DOI: 10.1021/jz100665c  0.6
2010 Lawrenz M, Wereszczynski J, Amaro R, Walker R, Roitberg A, McCammon JA. Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy Proteins: Structure, Function and Bioinformatics. 78: 2523-2532. PMID 20602360 DOI: 10.1002/prot.22761  1
2010 Lu B, Cheng X, Huang J, McCammon JA. AFMPB: An Adaptive Fast Multipole Poisson-Boltzmann Solver for Calculating Electrostatics in Biomolecular Systems. Computer Physics Communications. 181: 1150-1160. PMID 20532187 DOI: 10.1016/j.cpc.2010.02.015  1
2010 Durrant JD, Urbaniak MD, Ferguson MA, McCammon JA. Computer-aided identification of Trypanosoma brucei uridine diphosphate galactose 4'-epimerase inhibitors: toward the development of novel therapies for African sleeping sickness. Journal of Medicinal Chemistry. 53: 5025-32. PMID 20527952 DOI: 10.1021/jm100456a  1
2010 Rouffet M, de Oliveira CA, Udi Y, Agrawal A, Sagi I, McCammon JA, Cohen SM. From sensors to silencers: quinoline- and benzimidazole-sulfonamides as inhibitors for zinc proteases. Journal of the American Chemical Society. 132: 8232-3. PMID 20507095 DOI: 10.1021/ja101088j  1
2010 Durrant JD, Keränen H, Wilson BA, McCammon JA. Computational identification of uncharacterized cruzain binding sites. Plos Neglected Tropical Diseases. 4: e676. PMID 20485483 DOI: 10.1371/journal.pntd.0000676  1
2010 Tainer JA, McCammon JA, Ivanov I. Recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading Journal of the American Chemical Society. 132: 7372-7378. PMID 20455582 DOI: 10.1021/ja100365x  1
2010 Bauler P, Huber G, Leyh T, McCammon JA. Channeling by Proximity: The Catalytic Advantages of Active Site Colocalization Using Brownian Dynamics. The Journal of Physical Chemistry Letters. 1: 1332-1335. PMID 20454551 DOI: 10.1021/jz1002007  0.76
2010 Durrant JD, McCammon JA. Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug design. Computational Biology and Chemistry. 34: 97-105. PMID 20427241 DOI: 10.1016/j.compbiolchem.2010.03.005  1
2010 Qin S, Minh DD, McCammon JA, Zhou HX. Method to Predict Crowding Effects by Postprocessing Molecular Dynamics Trajectories: Application to the Flap Dynamics of HIV-1 Protease. The Journal of Physical Chemistry Letters. 1: 107-110. PMID 20228897 DOI: 10.1021/jz900023w  1
2010 Li B, Lu B, Wang Z, McCammon JA. Solutions to a reduced Poisson-Nernst-Planck system and determination of reaction rates. Physica A. 389: 1329-1345. PMID 20228879 DOI: 10.1016/j.physa.2009.12.024  0.84
2010 Sung JC, Van Wynsberghe AW, Amaro RE, Li WW, McCammon JA. Role of secondary sialic acid binding sites in influenza N1 neuraminidase. Journal of the American Chemical Society. 132: 2883-5. PMID 20155919 DOI: 10.1021/ja9073672  0.52
2010 Durrant JD, Amaro RE, Xie L, Urbaniak MD, Ferguson MA, Haapalainen A, Chen Z, Di Guilmi AM, Wunder F, Bourne PE, McCammon JA. A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. Plos Computational Biology. 6: e1000648. PMID 20098496 DOI: 10.1371/journal.pcbi.1000648  1
2010 Perryman AL, Forli S, Morris GM, Burt C, Cheng Y, Palmer MJ, Whitby K, McCammon JA, Phillips C, Olson AJ. A dynamic model of HIV integrase inhibition and drug resistance. Journal of Molecular Biology. 397: 600-15. PMID 20096702 DOI: 10.1016/j.jmb.2010.01.033  1
2010 Markwick PR, Cervantes CF, Abel BL, Komives EA, Blackledge M, McCammon JA. Enhanced conformational space sampling improves the prediction of chemical shifts in proteins. Journal of the American Chemical Society. 132: 1220-1. PMID 20063881 DOI: 10.1021/ja9093692  1
2010 Grant BJ, Gorfe AA, McCammon JA. Large conformational changes in proteins: signaling and other functions. Current Opinion in Structural Biology. 20: 142-7. PMID 20060708 DOI: 10.1016/j.sbi.2009.12.004  0.76
2010 Sivendran S, Jones V, Sun D, Wang Y, Grzegorzewicz AE, Scherman MS, Napper AD, McCammon JA, Lee RE, Diamond SL, McNeil M. Identification of triazinoindol-benzimidazolones as nanomolar inhibitors of the Mycobacterium tuberculosis enzyme TDP-6-deoxy-d-xylo-4-hexopyranosid-4-ulose 3,5-epimerase (RmlC). Bioorganic & Medicinal Chemistry. 18: 896-908. PMID 19969466 DOI: 10.1016/j.bmc.2009.11.033  1
2010 Zhou HX, McCammon JA. The gates of ion channels and enzymes Trends in Biochemical Sciences. 35: 179-185. PMID 19926290 DOI: 10.1016/j.tibs.2009.10.007  1
2010 Durrant JD, de Oliveira CA, McCammon JA. Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitors. Journal of Molecular Recognition : Jmr. 23: 173-82. PMID 19882751 DOI: 10.1002/jmr.989  1
2010 Lu B, McCammon JA. Kinetics of diffusion-controlled enzymatic reactions with charged substrates Pmc Biophysics. 3. DOI: 10.1186/1757-5036-3-1  1
2010 Wereszczynski J, McCammon JA. Using selectively applied accelerated molecular dynamics to enhance free energy calculations Journal of Chemical Theory and Computation. 6: 3285-3292. DOI: 10.1021/ct100322t  1
2010 Setny P, Baron R, McCammon JA. How can hydrophobic association be enthalpy driven? Journal of Chemical Theory and Computation. 6: 2866-2871. DOI: 10.1021/ct1003077  1
2010 Huber GA, McCammon JA. Browndye: A software package for Brownian dynamics Computer Physics Communications. 181: 1896-1905. DOI: 10.1016/j.cpc.2010.07.022  1
2009 Cheng LT, Xie Y, Dzubiella J, McCammon JA, Che J, Li B. Coupling the Level-Set Method with Molecular Mechanics for Variational Implicit Solvation of Nonpolar Molecules. Journal of Chemical Theory and Computation. 5: 257-266. PMID 20150952 DOI: 10.1021/ct800297d  1
2009 Markwick PR, Bouvignies G, Salmon L, McCammon JA, Nilges M, Blackledge M. Toward a unified representation of protein structural dynamics in solution. Journal of the American Chemical Society. 131: 16968-75. PMID 19919148 DOI: 10.1021/ja907476w  1
2009 Setny P, Wang Z, Cheng LT, Li B, McCammon JA, Dzubiella J. Dewetting-controlled binding of ligands to hydrophobic pockets. Physical Review Letters. 103: 187801. PMID 19905832 DOI: 10.1103/PhysRevLett.103.187801  1
2009 Baron R, McCammon JA, Mattevi A. The oxygen-binding vs. oxygen-consuming paradigm in biocatalysis: structural biology and biomolecular simulation. Current Opinion in Structural Biology. 19: 672-9. PMID 19896366 DOI: 10.1016/j.sbi.2009.10.003  0.76
2009 Newhouse EI, Xu D, Markwick PR, Amaro RE, Pao HC, Wu KJ, Alam M, McCammon JA, Li WW. Mechanism of glycan receptor recognition and specificity switch for avian, swine, and human adapted influenza virus hemagglutinins: a molecular dynamics perspective. Journal of the American Chemical Society. 131: 17430-42. PMID 19891427 DOI: 10.1021/ja904052q  1
2009 Khavrutskii IV, Grant B, Taylor SS, McCammon JA. A transition path ensemble study reveals a linchpin role for Mg(2+) during rate-limiting ADP release from protein kinase A. Biochemistry. 48: 11532-45. PMID 19886670 DOI: 10.1021/bi901475g  1
2009 Cheng LT, Wang Z, Setny P, Dzubiella J, Li B, McCammon JA. Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach. The Journal of Chemical Physics. 131: 144102. PMID 19831428 DOI: 10.1063/1.3242274  1
2009 Cervantes CF, Markwick PR, Sue SC, McCammon JA, Dyson HJ, Komives EA. Functional dynamics of the folded ankyrin repeats of I kappa B alpha revealed by nuclear magnetic resonance. Biochemistry. 48: 8023-31. PMID 19591507 DOI: 10.1021/bi900712r  1
2009 Baron R, Riley C, Chenprakhon P, Thotsaporn K, Winter RT, Alfieri A, Forneris F, van Berkel WJ, Chaiyen P, Fraaije MW, Mattevi A, McCammon JA. Multiple pathways guide oxygen diffusion into flavoenzyme active sites. Proceedings of the National Academy of Sciences of the United States of America. 106: 10603-8. PMID 19541622 DOI: 10.1073/pnas.0903809106  0.76
2009 Lu B, Cheng X, Huang J, McCammon JA. An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics. Journal of Chemical Theory and Computation. 5: 1692-1699. PMID 19517026 DOI: 10.1021/ct900083k  1
2009 Cheng X, Ivanov I, Wang H, Sine SM, McCammon JA. Molecular-dynamics simulations of ELIC-a prokaryotic homologue of the nicotinic acetylcholine receptor. Biophysical Journal. 96: 4502-13. PMID 19486673 DOI: 10.1016/j.bpj.2009.03.018  1
2009 Lawrenz M, Baron R, McCammon JA. Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. Journal of Chemical Theory and Computation. 5: 1106-1116. PMID 19461872 DOI: 10.1021/ct800559d  1
2009 Wong S, Amaro RE, McCammon JA. MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein Interface. Journal of Chemical Theory and Computation. 5: 422-429. PMID 19461869 DOI: 10.1021/ct8003707  0.52
2009 Burke JE, Babakhani A, Gorfe AA, Kokotos G, Li S, Woods VL, McCammon JA, Dennis EA. Location of inhibitors bound to group IVA phospholipase A2 determined by molecular dynamics and deuterium exchange mass spectrometry. Journal of the American Chemical Society. 131: 8083-91. PMID 19459633 DOI: 10.1021/ja900098y  1
2009 Knight JD, Hamelberg D, McCammon JA, Kothary R. The role of conserved water molecules in the catalytic domain of protein kinases. Proteins. 76: 527-35. PMID 19425109 DOI: 10.1002/prot.22451  1
2009 Fajer M, Swift RV, McCammon JA. Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics. Journal of Computational Chemistry. 30: 1719-25. PMID 19421994 DOI: 10.1002/jcc.21285  1
2009 McCammon JA. Darwinian biophysics: Electrostatics and evolution in the kinetics of molecular binding Proceedings of the National Academy of Sciences of the United States of America. 106: 7683-7684. PMID 19416830 DOI: 10.1073/pnas.0902767106  1
2009 Wang HL, Toghraee R, Papke D, Cheng XL, McCammon JA, Ravaioli U, Sine SM. Single-channel current through nicotinic receptor produced by closure of binding site C-loop. Biophysical Journal. 96: 3582-90. PMID 19413963 DOI: 10.1016/j.bpj.2009.02.020  1
2009 Xu D, Newhouse EI, Amaro RE, Pao HC, Cheng LS, Markwick PR, McCammon JA, Li WW, Arzberger PW. Distinct glycan topology for avian and human sialopentasaccharide receptor analogues upon binding different hemagglutinins: a molecular dynamics perspective. Journal of Molecular Biology. 387: 465-91. PMID 19356594 DOI: 10.1016/j.jmb.2009.01.040  1
2009 Lu S, Michailova A, Saucerman J, Cheng Y, Yu Z, Kaiser T, Li W, Bank R, Holst M, McCammon J, Hayashi T, Hoshijima M, Arzberger P, McCulloch A. Multiscale modeling in rodent ventricular myocytes. Ieee Engineering in Medicine and Biology Magazine : the Quarterly Magazine of the Engineering in Medicine & Biology Society. 28: 46-57. PMID 19349251 DOI: 10.1109/MEMB.2009.931787  1
2009 Ivetac A, McCammon JA. Elucidating the Inhibition Mechanism of HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors through Multicopy Molecular Dynamics Simulations Journal of Molecular Biology. 388: 644-658. PMID 19324058 DOI: 10.1016/j.jmb.2009.03.037  1
2009 Swift RV, McCammon JA. Substrate induced population shifts and stochastic gating in the PBCV-1 mRNA capping enzyme. Journal of the American Chemical Society. 131: 5126-33. PMID 19301911 DOI: 10.1021/ja808064g  1
2009 Grant BJ, Gorfe AA, McCammon JA. Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. Plos Computational Biology. 5: e1000325. PMID 19300489 DOI: 10.1371/journal.pcbi.1000325  0.76
2009 Amaro RE, Cheng X, Ivanov I, Xu D, McCammon JA. Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations. Journal of the American Chemical Society. 131: 4702-9. PMID 19296611 DOI: 10.1021/ja8085643  1
2009 Cheng Y, Holst MJ, McCammon JA. Finite element analysis of drug electrostatic diffusion: inhibition rate studies in N1 neuraminidase. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 281-92. PMID 19209708 DOI: 10.1142/9789812836939_0027  1
2009 Durrant JD, Amaro RE, McCammon JA. AutoGrow: a novel algorithm for protein inhibitor design. Chemical Biology & Drug Design. 73: 168-78. PMID 19207419 DOI: 10.1111/j.1747-0285.2008.00761.x  1
2009 Babakhani A, Talley TT, Taylor P, McCammon JA. A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach. Computational Biology and Chemistry. 33: 160-70. PMID 19186108 DOI: 10.1016/j.compbiolchem.2008.12.002  1
2009 Agrawal A, de Oliveira CA, Cheng Y, Jacobsen JA, McCammon JA, Cohen SM. Thioamide hydroxypyrothiones supersede amide hydroxypyrothiones in potency against anthrax lethal factor. Journal of Medicinal Chemistry. 52: 1063-74. PMID 19170530 DOI: 10.1021/jm8013212  1
2009 Khavrutskii IV, Gorfe AA, Lu B, McCammon JA. Free energy for the permeation of Na(+) and Cl(-) ions and their ion-pair through a zwitterionic dimyristoyl phosphatidylcholine lipid bilayer by umbrella integration with harmonic fourier beads. Journal of the American Chemical Society. 131: 1706-16. PMID 19146415 DOI: 10.1021/ja8081704  1
2009 Swift RV, Durrant J, Amaro RE, McCammon JA. Toward understanding the conformational dynamics of RNA ligation. Biochemistry. 48: 709-19. PMID 19133737 DOI: 10.1021/bi8018114  1
2008 Khavrutskii IV, Fajer M, McCammon JA. Intrinsic Free Energy of the Conformational Transition of the KcsA Signature Peptide from Conducting to Nonconducting State. Journal of Chemical Theory and Computation. 4: 1541-1554. PMID 20357907 DOI: 10.1021/ct800086s  1
2008 Fajer M, Hamelberg D, McCammon JA. Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration. Journal of Chemical Theory and Computation. 4: 1565-1569. PMID 19461870 DOI: 10.1021/ct800250m  1
2008 de Oliveira CA, Hamelberg D, McCammon JA. Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations. Journal of Chemical Theory and Computation. 4: 1516-1525. PMID 19461868 DOI: 10.1021/ct800160q  1
2008 Baron R, Wong SE, de Oliveira CA, McCammon JA. E9-Im9 colicin DNase-immunity protein biomolecular association in water: a multiple-copy and accelerated molecular dynamics simulation study. The Journal of Physical Chemistry. B. 112: 16802-14. PMID 19053689 DOI: 10.1021/jp8061543  0.76
2008 Amaro RE, Schnaufer A, Interthal H, Hol W, Stuart KD, McCammon JA. Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei. Proceedings of the National Academy of Sciences of the United States of America. 105: 17278-83. PMID 18981420 DOI: 10.1073/pnas.0805820105  1
2008 Yu Z, Holst MJ, Hayashi T, Bajaj CL, Ellisman MH, McCammon JA, Hoshijima M. Three-dimensional geometric modeling of membrane-bound organelles in ventricular myocytes: bridging the gap between microscopic imaging and mathematical simulation. Journal of Structural Biology. 164: 304-13. PMID 18835449 DOI: 10.1016/j.jsb.2008.09.004  1
2008 Gorfe AA, McCammon JA. Similar membrane affinity of mono- and di-S-acylated ras membrane anchors: A new twist in the role of protein lipidation Journal of the American Chemical Society. 130: 12624-12625. PMID 18761454 DOI: 10.1021/ja805110q  1
2008 Cheng Y, Chang CE, Yu Z, Zhang Y, Sun M, Leyh TS, Holst MJ, McCammon JA. Diffusional channeling in the sulfate-activating complex: combined continuum modeling and coarse-grained brownian dynamics studies. Biophysical Journal. 95: 4659-67. PMID 18689458 DOI: 10.1529/biophysj.108.140038  1
2008 Babakhani A, Gorfe AA, Kim JE, McCammon JA. Thermodynamics of peptide insertion and aggregation in a lipid bilayer. The Journal of Physical Chemistry. B. 112: 10528-34. PMID 18681475 DOI: 10.1021/jp804710v  1
2008 Cheng YH, Cheng XL, Radić Z, McCammon JA. Acetylcholinesterase: mechanisms of covalent inhibition of H447I mutant determined by computational analyses. Chemico-Biological Interactions. 175: 196-9. PMID 18657802 DOI: 10.1016/j.cbi.2008.04.044  1
2008 Mura C, McCammon JA. Molecular dynamics of a kappaB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation. Nucleic Acids Research. 36: 4941-55. PMID 18653524 DOI: 10.1093/nar/gkn473  1
2008 Gorfe AA, Baron R, McCammon JA. Water-membrane partition thermodynamics of an amphiphilic lipopeptide: An enthalpy-driven hydrophobic effect Biophysical Journal. 95: 3269-3277. PMID 18621822 DOI: 10.1529/biophysj.108.136481  1
2008 Cheng LS, Amaro RE, Xu D, Li WW, Arzberger PW, McCammon JA. Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. Journal of Medicinal Chemistry. 51: 3878-94. PMID 18558668 DOI: 10.1021/jm8001197  1
2008 Gorfe AA, Grant BJ, McCammon JA. Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins. Structure (London, England : 1993). 16: 885-96. PMID 18547521 DOI: 10.1016/j.str.2008.03.009  0.76
2008 Wong SE, Baron R, McCammon JA. Hot-spot residues at the E9/Im9 interface help binding via different mechanisms. Biopolymers. 89: 916-20. PMID 18546205 DOI: 10.1002/bip.21035  0.76
2008 Chang CE, McLaughlin WA, Baron R, Wang W, McCammon JA. Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association. Proceedings of the National Academy of Sciences of the United States of America. 105: 7456-61. PMID 18495919 DOI: 10.1073/pnas.0800452105  1
2008 Baron R, McCammon JA. (Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding Chemphyschem. 9: 983-988. PMID 18418822 DOI: 10.1002/cphc.200700857  1
2008 Yu Z, Holst MJ, Cheng Y, McCammon JA. Feature-preserving adaptive mesh generation for molecular shape modeling and simulation. Journal of Molecular Graphics & Modelling. 26: 1370-80. PMID 18337134 DOI: 10.1016/j.jmgm.2008.01.007  1
2008 Swift RV, McCammon JA. Catalytically requisite conformational dynamics in the mRNA-capping enzyme probed by targeted molecular dynamics. Biochemistry. 47: 4102-11. PMID 18330997 DOI: 10.1021/bi8000209  1
2008 Wang HL, Cheng X, Taylor P, McCammon JA, Sine SM. Control of cation permeation through the nicotinic receptor channel. Plos Computational Biology. 4: e41. PMID 18282090 DOI: 10.1371/journal.pcbi.0040041  1
2008 Che J, Dzubiella J, Li B, McCammon JA. Electrostatic free energy and its variations in implicit solvent models. The Journal of Physical Chemistry. B. 112: 3058-69. PMID 18275182 DOI: 10.1021/jp7101012  1
2008 Abankwa D, Hanzal-Bayer M, Ariotti N, Plowman SJ, Gorfe AA, Parton RG, McCammon JA, Hancock JF. A novel switch region regulates H-ras membrane orientation and signal output. The Embo Journal. 27: 727-35. PMID 18273062 DOI: 10.1038/emboj.2008.10  0.68
2008 Gunatilleke SS, de Oliveira CA, McCammon JA, Barrios AM. Inhibition of cathepsin B by Au(I) complexes: a kinetic and computational study. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 13: 555-61. PMID 18253767 DOI: 10.1007/s00775-008-0344-0  1
2008 Khavrutskii IV, Dzubiella J, McCammon JA. Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method. The Journal of Chemical Physics. 128: 044106. PMID 18247929 DOI: 10.1063/1.2825620  1
2008 Amaro RE, Baron R, McCammon JA. An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. Journal of Computer-Aided Molecular Design. 22: 693-705. PMID 18196463 DOI: 10.1007/s10822-007-9159-2  1
2008 Minh DD, McCammon JA. Springs and speeds in free energy reconstruction from irreversible single-molecule pulling experiments. The Journal of Physical Chemistry. B. 112: 5892-7. PMID 18088108 DOI: 10.1021/jp0733163  0.88
2008 Zhou YC, Lu B, Huber GA, Holst MJ, McCammon JA. Continuum simulations of acetylcholine consumption by acetylcholinesterase: a Poisson-Nernst-Planck approach. The Journal of Physical Chemistry. B. 112: 270-5. PMID 18052268 DOI: 10.1021/jp074900e  1
2008 Gorfe AA, Chang CE, Ivanov I, McCammon JA. Dynamics of the acetylcholinesterase tetramer. Biophysical Journal. 94: 1144-54. PMID 17921202 DOI: 10.1529/biophysj.107.117879  0.88
2008 Yu Z, Holst MJ, Andrew McCammon J. High-fidelity geometric modeling for biomedical applications Finite Elements in Analysis and Design. 44: 715-723. DOI: 10.1016/j.finel.2008.03.004  0.52
2007 Swanson JM, Wagoner JA, Baker NA, McCammon JA. Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies:  Lessons Learned with Atom-Centered Dielectric Functions. Journal of Chemical Theory and Computation. 3: 170-83. PMID 26627162 DOI: 10.1021/ct600216k  1
2007 Mongan J, Simmerling C, McCammon JA, Case DA, Onufriev A. Generalized Born model with a simple, robust molecular volume correction. Journal of Chemical Theory and Computation. 3: 156-169. PMID 21072141 DOI: 10.1021/ct600085e  0.96
2007 Leduc PR, Wong MS, Ferreira PM, Groff RE, Haslinger K, Koonce MP, Lee WY, Love JC, McCammon JA, Monteiro-Riviere NA, Rotello VM, Rubloff GW, Westervelt R, Yoda M. Towards an in vivo biologically inspired nanofactory. Nature Nanotechnology. 2: 3-7. PMID 18654192 DOI: 10.1038/nnano.2006.180  1
2007 Lu B, Cheng X, McCammon JA. "New-version-fast-multipole-method" accelerated electrostatic interactions in biomolecular systems. Journal of Computational Physics. 226: 1348-1366. PMID 18379638 DOI: 10.1016/j.jcp.2007.05.026  0.68
2007 Amaro RE, Swift RV, McCammon JA. Functional and structural insights revealed by molecular dynamics simulations of an essential RNA editing ligase in Trypanosoma brucei. Plos Neglected Tropical Diseases. 1: e68. PMID 18060084 DOI: 10.1371/journal.pntd.0000068  1
2007 de Oliveira CA, Hamelberg D, McCammon JA. Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study. The Journal of Chemical Physics. 127: 175105. PMID 17994855 DOI: 10.1063/1.2794763  1
2007 Hamelberg D, de Oliveira CA, McCammon JA. Sampling of slow diffusive conformational transitions with accelerated molecular dynamics. The Journal of Chemical Physics. 127: 155102. PMID 17949218 DOI: 10.1063/1.2789432  1
2007 Cerutti DS, Baker NA, McCammon JA. Solvent reaction field potential inside an uncharged globular protein: a bridge between implicit and explicit solvent models? The Journal of Chemical Physics. 127: 155101. PMID 17949217 DOI: 10.1063/1.2771171  0.96
2007 Minh DD, Hamelberg D, McCammon JA. Accelerated entropy estimates with accelerated dynamics. The Journal of Chemical Physics. 127: 154105. PMID 17949130 DOI: 10.1063/1.2794754  0.88
2007 Lu B, Zhou YC, Huber GA, Bond SD, Holst MJ, McCammon JA. Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution. The Journal of Chemical Physics. 127: 135102. PMID 17919055 DOI: 10.1063/1.2775933  1
2007 Khavrutskii IV, McCammon JA. Generalized gradient-augmented harmonic Fourier beads method with multiple atomic and/or center-of-mass positional restraints. The Journal of Chemical Physics. 127: 124901. PMID 17902931 DOI: 10.1063/1.2771172  1
2007 Gorfe AA, Babakhani A, McCammon JA. Free energy profile of H-ras membrane anchor upon membrane insertion. Angewandte Chemie (International Ed. in English). 46: 8234-7. PMID 17886310 DOI: 10.1002/anie.200702379  1
2007 Gorfe AA, Babakhani A, McCammon JA. H-ras protein in a bilayer: interaction and structure perturbation. Journal of the American Chemical Society. 129: 12280-6. PMID 17880077 DOI: 10.1021/ja073949v  1
2007 Hamelberg D, Shen T, McCammon JA. A proposed signaling motif for nuclear import in mRNA processing via the formation of arginine claw. Proceedings of the National Academy of Sciences of the United States of America. 104: 14947-51. PMID 17823247 DOI: 10.1073/pnas.0703151104  0.36
2007 Cheng LT, Dzubiella J, McCammon JA, Li B. Application of the level-set method to the implicit solvation of nonpolar molecules. The Journal of Chemical Physics. 127: 084503. PMID 17764265 DOI: 10.1063/1.2757169  1
2007 Baron R, McCammon JA. Dynamics, hydration, and motional averaging of a loop-gated artificial protein cavity: The W191G mutant of cytochrome c peroxidase in water as revealed by molecular dynamics simulations Biochemistry. 46: 10629-10642. PMID 17718514 DOI: 10.1021/bi700866x  1
2007 Cheng X, Ivanov I, Wang H, Sine SM, McCammon JA. Nanosecond-timescale conformational dynamics of the human alpha7 nicotinic acetylcholine receptor. Biophysical Journal. 93: 2622-34. PMID 17573436 DOI: 10.1529/biophysj.107.109843  1
2007 Ivanov I, Cheng X, Sine SM, McCammon JA. Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family. Journal of the American Chemical Society. 129: 8217-24. PMID 17552523 DOI: 10.1021/ja070778l  1
2007 Amaro RE, Minh DD, Cheng LS, Lindstrom WM, Olson AJ, Lin JH, Li WW, McCammon JA. Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design. Journal of the American Chemical Society. 129: 7764-5. PMID 17539643 DOI: 10.1021/ja0723535  0.96
2007 Cheng Y, Cheng X, Radić Z, McCammon JA. Acetylcholinesterase: mechanisms of covalent inhibition of wild-type and H447I mutant determined by computational analyses. Journal of the American Chemical Society. 129: 6562-70. PMID 17461584 DOI: 10.1021/ja070601r  1
2007 Grant BJ, McCammon JA, Caves LS, Cross RA. Multivariate analysis of conserved sequence-structure relationships in kinesins: coupling of the active site and a tubulin-binding sub-domain. Journal of Molecular Biology. 368: 1231-48. PMID 17399740 DOI: 10.1016/j.jmb.2007.02.049  0.76
2007 Trylska J, Tozzini V, Chang CE, McCammon JA. HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics. Biophysical Journal. 92: 4179-87. PMID 17384072 DOI: 10.1529/biophysj.106.100560  0.88
2007 Sørensen J, Hamelberg D, Schiøtt B, McCammon JA. Comparative MD analysis of the stability of transthyretin providing insight into the fibrillation mechanism. Biopolymers. 86: 73-82. PMID 17315201 DOI: 10.1002/bip.20705  1
2007 Chang CE, Trylska J, Tozzini V, McCammon JA. Binding pathways of ligands to HIV-1 protease: coarse-grained and atomistic simulations. Chemical Biology & Drug Design. 69: 5-13. PMID 17313452 DOI: 10.1111/j.1747-0285.2007.00464.x  0.88
2007 Cheng Y, Suen JK, Zhang D, Bond SD, Zhang Y, Song Y, Baker NA, Bajaj CL, Holst MJ, McCammon JA. Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophysical Journal. 92: 3397-406. PMID 17307827 DOI: 10.1529/biophysj.106.102533  1
2007 Cheng Y, Suen JK, Radić Z, Bond SD, Holst MJ, McCammon JA. Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction models. Biophysical Chemistry. 127: 129-39. PMID 17307283 DOI: 10.1016/j.bpc.2007.01.003  1
2007 Ivanov I, Tainer JA, McCammon JA. Unraveling the three-metal-ion catalytic mechanism of the DNA repair endonuclease IV Proceedings of the National Academy of Sciences of the United States of America. 104: 1465-1470. PMID 17242363 DOI: 10.1073/pnas.0603468104  1
2007 Ngo JC, Gullingsrud J, Giang K, Yeh MJ, Fu XD, Adams JA, McCammon JA, Ghosh G. SR protein kinase 1 is resilient to inactivation. Structure (London, England : 1993). 15: 123-33. PMID 17223538 DOI: 10.1016/j.str.2006.11.011  1
2007 Tozzini V, Trylska J, Chang CE, McCammon JA. Flap opening dynamics in HIV-1 protease explored with a coarse-grained model. Journal of Structural Biology. 157: 606-15. PMID 17029846 DOI: 10.1016/j.jsb.2006.08.005  0.88
2007 Lu B, McCammon JA. Improved boundary element methods for Poisson-Boltzmann electrostatic potential and force calculations Journal of Chemical Theory and Computation. 3: 1134-1142. DOI: 10.1021/ct700001x  1
2006 Tozzini V, Rocchia W, McCammon JA. Mapping all-atom models onto one-bead Coarse Grained Models: general properties and applications to a minimal polypeptide model. Journal of Chemical Theory and Computation. 2: 667-673. PMID 19461947 DOI: 10.1021/ct050294k  0.48
2006 Lu B, Cheng X, Huang J, McCammon JA. Order N algorithm for computation of electrostatic interactions in biomolecular systems. Proceedings of the National Academy of Sciences of the United States of America. 103: 19314-9. PMID 17148613 DOI: 10.1073/pnas.0605166103  1
2006 de Oliveira CA, Hamelberg D, McCammon JA. On the application of accelerated molecular dynamics to liquid water simulations. The Journal of Physical Chemistry. B. 110: 22695-701. PMID 17092018 DOI: 10.1021/jp062845o  1
2006 Ivanov I, Chapados BR, McCammon JA, Tainer JA. Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications. Nucleic Acids Research. 34: 6023-33. PMID 17071716 DOI: 10.1093/nar/gkl744  1
2006 Senapati S, Cheng Y, McCammon JA. In-situ synthesis of a tacrine-triazole-based inhibitor of acetylcholinesterase: configurational selection imposed by steric interactions. Journal of Medicinal Chemistry. 49: 6222-30. PMID 17034128 DOI: 10.1021/jm051132b  1
2006 Bui JM, McCammon JA. Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanism. Proceedings of the National Academy of Sciences of the United States of America. 103: 15451-6. PMID 17021015 DOI: 10.1073/pnas.0605355103  1
2006 Cheng X, Wang H, Grant B, Sine SM, McCammon JA. Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors. Plos Computational Biology. 2: e134. PMID 17009865 DOI: 10.1371/journal.pcbi.0020134  1
2006 Hamelberg D, Shen T, McCammon JA. Insight into the role of hydration on protein dynamics. The Journal of Chemical Physics. 125: 094905. PMID 16965117 DOI: 10.1063/1.2232131  1
2006 Jain T, Cerutti DS, McCammon JA. Configurational-bias sampling technique for predicting side-chain conformations in proteins. Protein Science : a Publication of the Protein Society. 15: 2029-39. PMID 16943441 DOI: 10.1110/ps.062165906  0.96
2006 Yang G, Trylska J, Tor Y, McCammon JA. Binding of aminoglycosidic antibiotics to the oligonucleotide A-site model and 30S ribosomal subunit: Poisson-Boltzmann model, thermal denaturation, and fluorescence studies. Journal of Medicinal Chemistry. 49: 5478-90. PMID 16942021 DOI: 10.1021/jm060288o  0.56
2006 Grant BJ, Rodrigues AP, ElSawy KM, McCammon JA, Caves LS. Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics (Oxford, England). 22: 2695-6. PMID 16940322 DOI: 10.1093/bioinformatics/btl461  0.76
2006 Lewis JA, Mongan J, McCammon JA, Cohen SM. Evaluation and binding-mode prediction of thiopyrone-based inhibitors of anthrax lethal factor. Chemmedchem. 1: 694-7. PMID 16902919 DOI: 10.1002/cmdc.200600102  0.96
2006 Cerutti DS, Jain T, McCammon JA. CIRSE: a solvation energy estimator compatible with flexible protein docking and design applications. Protein Science : a Publication of the Protein Society. 15: 1579-96. PMID 16815913 DOI: 10.1110/ps.051985106  0.96
2006 Shen T, Hamelberg D, McCammon JA. Elasticity of peptide omega bonds. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 73: 041908. PMID 16711837 DOI: 10.1103/PhysRevE.73.041908  1
2006 Adcock SA, McCammon JA. Molecular dynamics: Survey of methods for simulating the activity of proteins Chemical Reviews. 106: 1589-1615. PMID 16683746 DOI: 10.1021/cr040426m  1
2006 Hamacher K, Hübsch A, McCammon JA. A minimal model for stabilization of biomolecules by hydrocarbon cross-linking Journal of Chemical Physics. 124. PMID 16674170 DOI: 10.1063/1.2185645  1
2006 Minh DD, Chang CE, Trylska J, Tozzini V, McCammon JA. The influence of macromolecular crowding on HIV-1 protease internal dynamics. Journal of the American Chemical Society. 128: 6006-7. PMID 16669648 DOI: 10.1021/ja060483s  0.88
2006 Dzubiella J, Swanson JM, McCammon JA. Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models. Physical Review Letters. 96: 087802. PMID 16606226  1
2006 Chang CE, Shen T, Trylska J, Tozzini V, McCammon JA. Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model. Biophysical Journal. 90: 3880-5. PMID 16533835 DOI: 10.1529/biophysj.105.074575  1
2006 Cheng Y, Zhang Y, McCammon JA. How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: a theoretical study. Protein Science : a Publication of the Protein Society. 15: 672-83. PMID 16522793 DOI: 10.1110/ps.051852306  1
2006 Dzubiella J, Swanson JM, McCammon JA. Coupling nonpolar and polar solvation free energies in implicit solvent models. The Journal of Chemical Physics. 124: 084905. PMID 16512740 DOI: 10.1063/1.2171192  1
2006 Perryman AL, Lin JH, McCammon JA. Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug design. Biopolymers. 82: 272-84. PMID 16508951 DOI: 10.1002/bip.20497  0.96
2006 Zhang D, Gullingsrud J, McCammon JA. Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain. Journal of the American Chemical Society. 128: 3019-26. PMID 16506783 DOI: 10.1021/ja057292u  1
2006 Bui JM, Radic Z, Taylor P, McCammon JA. Conformational transitions in protein-protein association: binding of fasciculin-2 to acetylcholinesterase. Biophysical Journal. 90: 3280-7. PMID 16473897 DOI: 10.1529/biophysj.105.075564  1
2006 Ivanov I, Vemparala S, Pophristic V, Kuroda K, DeGrado WF, McCammon JA, Klein ML. Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamics. Journal of the American Chemical Society. 128: 1778-9. PMID 16464062 DOI: 10.1021/ja0564665  1
2006 Gullingsrud J, Kim C, Taylor SS, McCammon JA. Dynamic binding of PKA regulatory subunit RIα Structure. 14: 141-149. PMID 16407073 DOI: 10.1016/j.str.2005.09.019  1
2006 Vigil D, Lin JH, Sotriffer CA, Pennypacker JK, McCammon JA, Taylor SS. A simple electrostatic switch important in the activation of type I protein kinase A by cyclic AMP. Protein Science : a Publication of the Protein Society. 15: 113-21. PMID 16322564 DOI: 10.1110/ps.051723606  0.96
2006 Cheng X, Lu B, Grant B, Law RJ, McCammon JA. Channel opening motion of alpha7 nicotinic acetylcholine receptor as suggested by normal mode analysis. Journal of Molecular Biology. 355: 310-24. PMID 16307758 DOI: 10.1016/j.jmb.2005.10.039  1
2006 Giorgione JR, Lin JH, McCammon JA, Newton AC. Increased membrane affinity of the C1 domain of protein kinase Cdelta compensates for the lack of involvement of its C2 domain in membrane recruitment. The Journal of Biological Chemistry. 281: 1660-9. PMID 16293612 DOI: 10.1074/jbc.M510251200  0.96
2006 Konecny R, Trylska J, Tama F, Zhang D, Baker NA, Brooks CL, McCammon JA. Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers. 82: 106-20. PMID 16278831 DOI: 10.1002/bip.20409  1
2006 Gullingsrud J, Babakhani A, McCammon JA. Computational investigation of pressure profiles in lipid bilayers with embedded proteins Molecular Simulation. 32: 831-838. DOI: 10.1080/08927020600779350  1
2006 Hamacher K, McCammon JA. Computing the amino acid specificity of fluctuations in biomolecular systems Journal of Chemical Theory and Computation. 2: 873-878. DOI: 10.1021/ct050247s  1
2006 Hamelberg D, McCammon JA. Chapter 12 Accelerating Conformational Transitions in Biomolecular Simulations Annual Reports in Computational Chemistry. 2: 221-232. DOI: 10.1016/S1574-1400(06)02012-3  1
2005 Swanson JM, Adcock SA, McCammon JA. Optimized Radii for Poisson-Boltzmann Calculations with the AMBER Force Field. Journal of Chemical Theory and Computation. 1: 484-93. PMID 26641515 DOI: 10.1021/ct049834o  0.96
2005 Cerutti DS, Ten Eyck LF, McCammon JA. Rapid Estimation of Solvation Energy for Simulations of Protein-Protein Association. Journal of Chemical Theory and Computation. 1: 143-52. PMID 26641125 DOI: 10.1021/ct049946f  0.96
2005 Swanson JM, Mongan J, McCammon JA. Limitations of atom-centered dielectric functions in implicit solvent models. The Journal of Physical Chemistry. B. 109: 14769-72. PMID 16852866 DOI: 10.1021/jp052883s  0.96
2005 Bui JM, McCammon JA. Acetylcholinesterase: pivotal roles of its long omega loop (Cys69-Cys96) in regulating substrate binding. Chemico-Biological Interactions. 157: 357-9. PMID 16429484 DOI: 10.1016/j.cbi.2005.10.049  1
2005 Senapati S, Bui JM, McCammon JA. Induced fit in mouse acetylcholinesterase upon binding a femtomolar inhibitor: a molecular dynamics study. Journal of Medicinal Chemistry. 48: 8155-62. PMID 16366597 DOI: 10.1021/jm050669m  1
2005 Zhang D, McCammon JA. The association of tetrameric acetylcholinesterase with ColQ tail: a block normal mode analysis. Plos Computational Biology. 1: e62. PMID 16299589 DOI: 10.1371/journal.pcbi.0010062  1
2005 Wong CF, Kua J, Zhang Y, Straatsma TP, McCammon JA. Molecular docking of balanol to dynamics snapshots of protein kinase A. Proteins. 61: 850-8. PMID 16245317 DOI: 10.1002/prot.20688  1
2005 Puerta DT, Mongan J, Tran BL, McCammon JA, Cohen SM. Potent, selective pyrone-based inhibitors of stromelysin-1. Journal of the American Chemical Society. 127: 14148-9. PMID 16218585 DOI: 10.1021/ja054558o  0.96
2005 Hamelberg D, McCammon JA. Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease. Journal of the American Chemical Society. 127: 13778-9. PMID 16201784 DOI: 10.1021/ja054338a  1
2005 McCammon JA. Target flexibility in molecular recognition Biochimica Et Biophysica Acta - Proteins and Proteomics. 1754: 221-224. PMID 16181817 DOI: 10.1016/j.bbapap.2005.07.041  1
2005 Lu B, Cheng X, Hou T, McCammon JA. Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals. The Journal of Chemical Physics. 123: 084904. PMID 16164327 DOI: 10.1063/1.2008252  1
2005 Shen T, Zong C, Hamelberg D, McCammon JA, Wolynes PG. The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 19: 1389-95. PMID 16126906 DOI: 10.1096/fj.04-3590hyp  1
2005 Minh DD, Bui JM, Chang CE, Jain T, Swanson JM, McCammon JA. The entropic cost of protein-protein association: a case study on acetylcholinesterase binding to fasciculin-2. Biophysical Journal. 89: L25-7. PMID 16100267 DOI: 10.1529/biophysj.105.069336  1
2005 Trylska J, McCammon JA, Brooks Iii CL. Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach. Journal of the American Chemical Society. 127: 11125-33. PMID 16076220 DOI: 10.1021/ja052639e  0.56
2005 Lu B, Zhang D, McCammon JA. Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method. The Journal of Chemical Physics. 122: 214102. PMID 15974723 DOI: 10.1063/1.1924448  1
2005 Trylska J, Tozzini V, McCammon JA. Exploring global motions and correlations in the ribosome. Biophysical Journal. 89: 1455-63. PMID 15951386 DOI: 10.1529/biophysj.104.058495  0.56
2005 Law RJ, Henchman RH, McCammon JA. A gating mechanism proposed from a simulation of a human alpha7 nicotinic acetylcholine receptor. Proceedings of the National Academy of Sciences of the United States of America. 102: 6813-8. PMID 15857954 DOI: 10.1073/pnas.0407739102  1
2005 Sims PA, Wong CF, Vuga D, McCammon JA, Sefton BM. Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems. Journal of Computational Chemistry. 26: 668-81. PMID 15754303 DOI: 10.1002/jcc.20207  0.72
2005 Hamelberg D, Shen T, McCammon JA. Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis. Journal of the American Chemical Society. 127: 1969-74. PMID 15701032 DOI: 10.1021/ja0446707  1
2005 Cheng Y, Zhang Y, McCammon JA. How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study. Journal of the American Chemical Society. 127: 1553-62. PMID 15686389 DOI: 10.1021/ja0464084  1
2005 Henchman RH, Wang HL, Sine SM, Taylor P, McCammon JA. Ligand-induced conformational change in the alpha7 nicotinic receptor ligand binding domain. Biophysical Journal. 88: 2564-76. PMID 15665135 DOI: 10.1529/biophysj.104.053934  1
2005 Zhang D, Suen J, Zhang Y, Song Y, Radic Z, Taylor P, Holst MJ, Bajaj C, Baker NA, McCammon JA. Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophysical Journal. 88: 1659-65. PMID 15626705 DOI: 10.1529/biophysj.104.053850  1
2005 Gao F, Bren N, Burghardt TP, Hansen S, Henchman RH, Taylor P, McCammon JA, Sine SM. Agonist-mediated conformational changes in acetylcholine-binding protein revealed by simulation and intrinsic tryptophan fluorescence. The Journal of Biological Chemistry. 280: 8443-51. PMID 15591050 DOI: 10.1074/jbc.M412389200  1
2005 Dzubiella J, McCammon JA. Substrate concentration dependence of the diffusion-controlled steady-state rate constant Journal of Chemical Physics. 122. DOI: 10.1063/1.1887165  1
2005 Cerutti DS, Ten Eyck LF, McCammon JA. Rapid estimation of solvation energy for simulations of protein-protein association Journal of Chemical Theory and Computation. 1: 143-152. DOI: 10.1021/ct049946f  1
2005 McCammon JA, Wade RC. Theory and simulation: Pushing the limits Current Opinion in Structural Biology. 15: 135-136. DOI: 10.1016/j.sbi.2005.03.009  1
2005 Tozzini V, McCammon JA. A coarse grained model for the dynamics of flap opening in HIV-1 protease Chemical Physics Letters. 413: 123-128. DOI: 10.1016/j.cplett.2005.07.075  1
2005 McCammon JA. Computation of non-covalent binding affinities Theory and Applications of Computational Chemistry. 41-46. DOI: 10.1016/B978-044451719-7/50046-9  1
2004 Mongan J, Case DA, McCammon JA. Constant pH molecular dynamics in generalized Born implicit solvent. Journal of Computational Chemistry. 25: 2038-48. PMID 15481090 DOI: 10.1002/jcc.20139  0.96
2004 Zhang D, Konecny R, Baker NA, McCammon JA. Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach. Biopolymers. 75: 325-37. PMID 15386271 DOI: 10.1002/bip.20120  1
2004 Trylska J, Konecny R, Tama F, Brooks CL, McCammon JA. Ribosome motions modulate electrostatic properties. Biopolymers. 74: 423-31. PMID 15274086 DOI: 10.1002/bip.20093  0.68
2004 Hamelberg D, Mongan J, McCammon JA. Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. The Journal of Chemical Physics. 120: 11919-29. PMID 15268227 DOI: 10.1063/1.1755656  0.96
2004 Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research. 32: W665-7. PMID 15215472 DOI: 10.1093/nar/gkh381  0.96
2004 Hamelberg D, McCammon JA. Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method. Journal of the American Chemical Society. 126: 7683-9. PMID 15198616 DOI: 10.1021/ja0377908  1
2004 Bui JM, Tai K, McCammon JA. Acetylcholinesterase: enhanced fluctuations and alternative routes to the active site in the complex with fasciculin-2. Journal of the American Chemical Society. 126: 7198-205. PMID 15186156 DOI: 10.1021/ja0485715  1
2004 Sims PA, Wong CF, McCammon JA. Charge optimization of the interface between protein kinases and their ligands. Journal of Computational Chemistry. 25: 1416-29. PMID 15185335 DOI: 10.1002/jcc.20067  0.72
2004 Schames JR, Henchman RH, Siegel JS, Sotriffer CA, Ni H, McCammon JA. Discovery of a novel binding trench in HIV integrase. Journal of Medicinal Chemistry. 47: 1879-81. PMID 15055986 DOI: 10.1021/jm0341913  1
2004 Perryman AL, Lin JH, McCammon JA. HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs. Protein Science : a Publication of the Protein Society. 13: 1108-23. PMID 15044738 DOI: 10.1110/ps.03468904  0.96
2004 Song Y, Zhang Y, Shen T, Bajaj CL, McCammon JA, Baker NA. Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophysical Journal. 86: 2017-29. PMID 15041644 DOI: 10.1016/S0006-3495(04)74263-0  1
2004 Swanson JM, Henchman RH, McCammon JA. Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophysical Journal. 86: 67-74. PMID 14695250 DOI: 10.1016/S0006-3495(04)74084-9  1
2004 Vitalis A, Baker NA, McCammon JA. ISIM: A program for grand canonical Monte Carlo simulations of the ionic environment of biomolecules Molecular Simulation. 30: 45-61. DOI: 10.1080/08927020310001597862  1
2003 Kua J, Zhang Y, Eslami AC, Butler JR, McCammon JA. Studying the roles of W86, E202, and Y337 in binding of acetylcholine to acetylcholinesterase using a combined molecular dynamics and multiple docking approach. Protein Science : a Publication of the Protein Society. 12: 2675-84. PMID 14627729 DOI: 10.1110/ps.03318603  1
2003 Henchman RH, Wang HL, Sine SM, Taylor P, McCammon JA. Asymmetric structural motions of the homomeric alpha7 nicotinic receptor ligand binding domain revealed by molecular dynamics simulation. Biophysical Journal. 85: 3007-18. PMID 14581202 DOI: 10.1016/S0006-3495(03)74720-1  1
2003 Cerutti DS, Wong CF, McCammon JA. Brownian dynamics simulations of ion atmospheres around polyalanine and B-DNA: effects of biomolecular dielectric. Biopolymers. 70: 391-402. PMID 14579311 DOI: 10.1002/bip.10498  0.96
2003 Shen T, Wong CF, McCammon JA. Brownian dynamics simulation of helix-capping motifs. Biopolymers. 70: 252-9. PMID 14517913 DOI: 10.1002/bip.10466  1
2003 Bui JM, Henchman RH, McCammon JA. The dynamics of ligand barrier crossing inside the acetylcholinesterase gorge. Biophysical Journal. 85: 2267-72. PMID 14507691 DOI: 10.1016/S0006-3495(03)74651-7  1
2003 Sept D, Baker NA, McCammon JA. The physical basis of microtubule structure and stability. Protein Science : a Publication of the Protein Society. 12: 2257-61. PMID 14500883 DOI: 10.1110/ps.03187503  1
2003 Morikis D, Elcock AH, Jennings PA, McCammon JA. The pH dependence of stability of the activation helix and the catalytic site of GART. Biophysical Chemistry. 105: 279-91. PMID 14499900 DOI: 10.1016/S0301-4622(03)00079-6  1
2003 Nielsen JE, McCammon JA. Calculating pKa values in enzyme active sites. Protein Science : a Publication of the Protein Society. 12: 1894-901. PMID 12930989 DOI: 10.1110/ps.03114903  0.88
2003 Puerta DT, Schames JR, Henchman RH, McCammon JA, Cohen SM. From model complexes to metalloprotein inhibition: a synergistic approach to structure-based drug discovery. Angewandte Chemie (International Ed. in English). 42: 3772-4. PMID 12923840 DOI: 10.1002/anie.200351433  1
2003 Sims PA, Wong CF, McCammon JA. A computational model of binding thermodynamics: the design of cyclin-dependent kinase 2 inhibitors. Journal of Medicinal Chemistry. 46: 3314-25. PMID 12852762 DOI: 10.1021/jm0205043  0.72
2003 Shi J, Tai K, McCammon JA, Taylor P, Johnson DA. Nanosecond dynamics of the mouse acetylcholinesterase cys69-cys96 omega loop. The Journal of Biological Chemistry. 278: 30905-11. PMID 12759360 DOI: 10.1074/jbc.M303730200  1
2003 Tai K, Bond SD, MacMillan HR, Baker NA, Holst MJ, McCammon JA. Finite element simulations of acetylcholine diffusion in neuromuscular junctions. Biophysical Journal. 84: 2234-41. PMID 12668432 DOI: 10.1016/S0006-3495(03)75029-2  1
2003 Baker NA, McCammon JA. Electrostatic interactions. Methods of Biochemical Analysis. 44: 427-40. PMID 12647398  1
2003 Podtelezhnikov AA, Gao K, Bushman FD, McCammon JA. Modeling HIV-1 integrase complexes based on their hydrodynamic properties. Biopolymers. 68: 110-20. PMID 12579583 DOI: 10.1002/bip.10217  1
2003 Lin JH, Perryman AL, Schames JR, McCammon JA. The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers. 68: 47-62. PMID 12579579 DOI: 10.1002/bip.10218  0.96
2003 Nielsen JE, McCammon JA. On the evaluation and optimization of protein X-ray structures for pKa calculations. Protein Science : a Publication of the Protein Society. 12: 313-26. PMID 12538895 DOI: 10.1110/ps.0229903  0.88
2003 Wong CF, McCammon JA. Protein Flexibility and Computer-Aided Drug Design Annual Review of Pharmacology and Toxicology. 43: 31-45. PMID 12142469 DOI: 10.1146/annurev.pharmtox.43.100901.140216  1
2003 Zhang Y, McCammon JA. Studying the affinity and kinetics of molecular association with molecular-dynamics simulation Journal of Chemical Physics. 118: 1821-1827. DOI: 10.1063/1.1530162  1
2002 Perryman AL, McCammon JA. AutoDocking dinucleotides to the HIV-1 integrase core domain: exploring possible binding sites for viral and genomic DNA. Journal of Medicinal Chemistry. 45: 5624-7. PMID 12477345  0.96
2002 Rowley DC, Hansen MS, Rhodes D, Sotriffer CA, Ni H, McCammon JA, Bushman FD, Fenical W. Thalassiolins A-C: new marine-derived inhibitors of HIV cDNA integrase. Bioorganic & Medicinal Chemistry. 10: 3619-25. PMID 12213478 DOI: 10.1016/S0968-0896(02)00241-9  1
2002 Lin JH, Baker NA, McCammon JA. Bridging implicit and explicit solvent approaches for membrane electrostatics. Biophysical Journal. 83: 1374-9. PMID 12202363 DOI: 10.1016/S0006-3495(02)73908-8  0.96
2002 Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nature Structural Biology. 9: 646-52. PMID 12198485 DOI: 10.1038/nsb0902-646  1
2002 Zhang Y, Kua J, McCammon JA. Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study. Journal of the American Chemical Society. 124: 10572-7. PMID 12197759  1
2002 Henchman RH, McCammon JA. Structural and dynamic properties of water around acetylcholinesterase. Protein Science : a Publication of the Protein Society. 11: 2080-90. PMID 12192064 DOI: 10.1110/ps.0214002  1
2002 Shen T, Canino LS, McCammon JA. Unfolding proteins under external forces: a solvable model under the self-consistent pair contact probability approximation. Physical Review Letters. 89: 068103. PMID 12190614 DOI: 10.1103/PhysRevLett.89.068103  1
2002 Kua J, Zhang Y, McCammon JA. Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach. Journal of the American Chemical Society. 124: 8260-7. PMID 12105904  1
2002 Shen T, Tai K, Henchman RH, McCammon JA. Molecular dynamics of acetylcholinesterase. Accounts of Chemical Research. 35: 332-40. PMID 12069617  1
2002 Tai K, Shen T, Henchman RH, Bourne Y, Marchot P, McCammon JA. Mechanism of acetylcholinesterase inhibition by fasciculin: a 5-ns molecular dynamics simulation. Journal of the American Chemical Society. 124: 6153-61. PMID 12022850  1
2002 Lin JH, Perryman AL, Schames JR, McCammon JA. Computational drug design accommodating receptor flexibility: the relaxed complex scheme. Journal of the American Chemical Society. 124: 5632-3. PMID 12010024  0.96
2002 Henchman RH, McCammon JA. Extracting hydration sites around proteins from explicit water simulations. Journal of Computational Chemistry. 23: 861-9. PMID 11984847 DOI: 10.1002/jcc.10074  1
2002 Henchman RH, Tai K, Shen T, McCammon JA. Properties of water molecules in the active site gorge of acetylcholinesterase from computer simulation. Biophysical Journal. 82: 2671-82. PMID 11964254 DOI: 10.1016/S0006-3495(02)75609-9  1
2002 Ma C, Baker NA, Joseph S, McCammon JA. Binding of aminoglycoside antibiotics to the small ribosomal subunit: a continuum electrostatics investigation. Journal of the American Chemical Society. 124: 1438-42. PMID 11841313 DOI: 10.1021/ja016830+  1
2002 Canino LS, Shen T, McCammon JA. Changes in flexibility upon binding: Application of the self-consistent pair contact probability method to protein-protein interactions Journal of Chemical Physics. 117: 9927-9933. DOI: 10.1063/1.1517605  1
2002 Sept D, Baker NA, McCammon JA. The structure and stability of microtubules Annual International Conference of the Ieee Engineering in Medicine and Biology - Proceedings. 1: 363.  1
2001 Morikis D, Elcock AH, Jennings PA, McCammon JA. Proton transfer dynamics of GART: the pH-dependent catalytic mechanism examined by electrostatic calculations. Protein Science : a Publication of the Protein Society. 10: 2379-92. PMID 11604543 DOI: 10.1110/ps.17301  1
2001 Morikis D, Elcock AH, Jennings PA, McCammon JA. Native-state conformational dynamics of GART: a regulatory pH-dependent coil-helix transition examined by electrostatic calculations. Protein Science : a Publication of the Protein Society. 10: 2363-78. PMID 11604542 DOI: 10.1110/ps.17201  1
2001 Andrianantoandro E, Blanchoin L, Sept D, McCammon JA, Pollard TD. Kinetic mechanism of end-to-end annealing of actin filaments. Journal of Molecular Biology. 312: 721-30. PMID 11575927 DOI: 10.1006/jmbi.2001.5005  1
2001 Shen T, Wong CF, McCammon JA. Atomistic Brownian dynamics simulation of peptide phosphorylation Journal of the American Chemical Society. 123: 9107-9111. PMID 11552818 DOI: 10.1021/ja010190t  1
2001 Ni H, Sotriffer CA, McCammon JA. Ordered water and ligand mobility in the HIV-1 integrase-5CITEP complex: a molecular dynamics study. Journal of Medicinal Chemistry. 44: 3043-7. PMID 11543671 DOI: 10.1021/jm010205y  0.32
2001 Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: Application to microtubules and the ribosome Proceedings of the National Academy of Sciences of the United States of America. 98: 10037-10041. PMID 11517324 DOI: 10.1073/pnas.181342398  1
2001 Tai K, Shen T, Börjesson U, Philippopoulos M, McCammon JA. Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase. Biophysical Journal. 81: 715-24. PMID 11463620 DOI: 10.1016/S0006-3495(01)75736-0  1
2001 Sept D, McCammon JA. Thermodynamics and kinetics of actin filament nucleation Biophysical Journal. 81: 667-674. PMID 11463615 DOI: 10.1016/S0006-3495(01)75731-1  1
2001 Ondrechen MJ, Briggs JM, McCammon JA. A model for enzyme-substrate interaction in alanine racemase. Journal of the American Chemical Society. 123: 2830-4. PMID 11456969 DOI: 10.1021/ja0029679  1
2001 Wong CF, Hünenberger PH, Akamine P, Narayana N, Diller T, McCammon JA, Taylor S, Xuong NH. Computational analysis of PKA-balanol interactions Journal of Medicinal Chemistry. 44: 1530-1539. PMID 11334563 DOI: 10.1021/jm000443d  1
2001 Shen TY, Tai K, McCammon JA. Statistical analysis of the fractal gating motions of the enzyme acetylcholinesterase. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 63: 041902. PMID 11308872 DOI: 10.1103/PhysRevE.63.041902  1
2001 Elcock AH, McCammon JA. Identification of protein oligomerization states by analysis of interface conservation Proceedings of the National Academy of Sciences of the United States of America. 98: 2990-2994. PMID 11248019 DOI: 10.1073/pnas.061411798  1
2001 Nolen B, Yun CY, Wong CF, McCammon JA, Fu XD, Ghosh G. The structure of Sky1p reveals a novel mechanism for constitutive activity. Nature Structural Biology. 8: 176-83. PMID 11175909 DOI: 10.1038/84178  0.48
2001 Elcock AH, McCammon JA. Calculation of weak protein-protein interactions: The pH dependence of the second virial coefficient Biophysical Journal. 80: 613-625. PMID 11159430 DOI: 10.1016/S0006-3495(01)76042-0  1
2000 Carlson HA, Masukawa KM, Rubins K, Bushman FD, Jorgensen WL, Lins RD, Briggs JM, McCammon JA. Developing a dynamic pharmacophore model for HIV-1 integrase. Journal of Medicinal Chemistry. 43: 2100-14. PMID 10841789 DOI: 10.1021/jm990322h  1
2000 Brown FL, Leitner DM, McCammon JA, Wilson KR. Lateral diffusion of membrane proteins in the presence of static and dynamic corrals: suggestions for appropriate observables. Biophysical Journal. 78: 2257-69. PMID 10777724 DOI: 10.1016/S0006-3495(00)76772-5  0.52
2000 Wlodek ST, Shen T, McCammon JA. Electrostatic steering of substrate to acetylcholinesterase: Analysis of field fluctuations Biopolymers. 53: 265-271. PMID 10679631 DOI: 10.1002/(SICI)1097-0282(200003)53:3<265::AID-BIP6>3.0.CO;2-N  1
2000 Carlson HA, McCammon JA. Accommodating protein flexibility in computational drug design. Molecular Pharmacology. 57: 213-8. PMID 10648630  1
1999 Sept D, Elcock AH, McCammon JA. Computer simulations of actin polymerization can explain the barbed-pointed end asymmetry Journal of Molecular Biology. 294: 1181-1189. PMID 10600376 DOI: 10.1006/jmbi.1999.3332  1
1999 Sept D, Xu J, Pollard TD, McCammon JA. Annealing accounts for the length of actin filaments formed by spontaneous polymerization Biophysical Journal. 77: 2911-2919. PMID 10585915 DOI: 10.1016/S0006-3495(99)77124-9  1
1999 Blachut-Okrasi?ska E, Lesyng B, Briggs JM, McCammon JA, Antosiewicz JM. Poisson-Boltzmann model studies of molecular electrostatic properties of the cAMP-dependent protein kinase. European Biophysics Journal : Ebj. 28: 457-67. PMID 10460339  1
1999 Baker NA, Helms V, McCammon JA. Dynamical properties of fasciculin-2 Proteins: Structure, Function and Genetics. 36: 447-453. PMID 10450086 DOI: 10.1002/(SICI)1097-0134(19990901)36:4<447::AID-PROT8>3.0.CO;2-E  1
1999 Elcock AH, Gabdoulline RR, Wade RC, McCammon JA. Computer simulation of protein-protein association kinetics: Acetylcholinesterase-fasciculin Journal of Molecular Biology. 291: 149-162. PMID 10438612 DOI: 10.1006/jmbi.1999.2919  1
1999 Lins RD, Briggs JM, Straatsma TP, Carlson HA, Greenwald J, Choe S, McCammon JA. Molecular dynamics studies on the HIV-1 integrase catalytic domain. Biophysical Journal. 76: 2999-3011. PMID 10354426  1
1999 Hünenberger PH, McCammon JA. Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: A continuum electrostatics study Biophysical Chemistry. 78: 69-88. PMID 10343384 DOI: 10.1016/S0301-4622(99)00007-1  1
1999 Wriggers W, Milligan RA, McCammon JA. Situs: A package for docking crystal structures into low-resolution maps from electron microscopy Journal of Structural Biology. 125: 185-195. PMID 10222274 DOI: 10.1006/jsbi.1998.4080  1
1999 Xavier KA, McDonald SM, McCammon JA, Willson RC. Association and dissociation kinetics of bobwhite quail lysozyme with monoclonal antibody HyHEL-5. Protein Engineering. 12: 79-83. PMID 10065714 DOI: 10.1093/protein/12.1.79  1
1999 Smart JL, McCammon JA. Phosphorylation stabilizes the N-termini of α-helices Biopolymers. 49: 225-233. PMID 9990840 DOI: 10.1002/(sici)1097-0282(199903)49:3<225::aid-bip4>3.0.co;2-b  1
1999 Carlson HA, Briggs JM, McCammon JA. Calculation of the pKa values for the ligands and side chains of Escherichia coli D-alanine:D-alanine ligase. Journal of Medicinal Chemistry. 42: 109-17. PMID 9888837 DOI: 10.1021/jm980351c  1
1999 Kirchhoff PD, Dutasta JP, Collet A, McCammon JA. Dynamic and rotational analysis of cryptophane host - Guest systems: Challenges of describing molecular recognition Journal of the American Chemical Society. 121: 381-390. DOI: 10.1021/ja981526a  1
1999 Huber GA, McCammon JA. OOMPAA - Object-Oriented Model for Probing Assemblages of Atoms Journal of Computational Physics. 151: 264-282. DOI: 10.1006/jcph.1999.6199  1
1999 Potter MJ, Kirchhoff PD, Carlson HA, Mccammon JA. Molecular dynamics of cryptophane and its complexes with tetramethylammonium and neopentane using a continuum solvent model Journal of Computational Chemistry. 20: 956-970.  1
1998 Weber W, Demirdjian H, Lins RD, Briggs JM, Ferreira R, McCammon JA. Brownian and essential dynamics studies of the HIV-1 integrase catalytic domain. Journal of Biomolecular Structure & Dynamics. 16: 733-45. PMID 10052629 DOI: 10.1080/07391102.1998.10508285  1
1998 Wriggers W, Milligan RA, Schulten K, McCammon JA. Self-organizing neural networks bridge the biomolecular resolution gap Journal of Molecular Biology. 284: 1247-1254. PMID 9878345 DOI: 10.1006/jmbi.1998.2232  1
1998 Tara S, Elcock AH, Kirchhoff PD, Briggs JM, Radic Z, Taylor P, McCammon JA. Rapid binding of a cationic active site inhibitor to wild type and mutant mouse acetylcholinesterase: Brownian dynamics simulation including diffusion in the active site gorge. Biopolymers. 46: 465-74. PMID 9838872 DOI: 10.1002/(SICI)1097-0282(199812)46:7<465::AID-BIP4>3.0.CO;2-Y  1
1998 Smart JL, McCammon JA. Analysis of synaptic transmission in the neuromuscular junction using a continuum finite element model Biophysical Journal. 75: 1679-1688. PMID 9746510 DOI: 10.1016/S0006-3495(98)77610-6  1
1998 Zhou HX, Wlodek ST, McCammon JA. Conformation gating as a mechanism for enzyme specificity. Proceedings of the National Academy of Sciences of the United States of America. 95: 9280-3. PMID 9689071 DOI: 10.1073/pnas.95.16.9280  0.52
1998 Elcock AH, McCammon JA. Electrostatic contributions to the stability of halophilic proteins Journal of Molecular Biology. 280: 731-748. PMID 9677300 DOI: 10.1006/jmbi.1998.1904  1
1998 McCammon JA. Theory of biomolecular recognition Current Opinion in Structural Biology. 8: 245-249. PMID 9631300 DOI: 10.1016/S0959-440X(98)80046-8  1
1998 Zhou HX, Briggs JM, Tara S, McCammon JA. Correlation between rate of enzyme-substrate diffusional encounter and average Boltzmann factor around active site. Biopolymers. 45: 355-60. PMID 9530014 DOI: 10.1002/(SICI)1097-0282(19980415)45:5<355::AID-BIP4>3.0.CO;2-K  1
1998 Fogolari F, Esposito G, Viglino P, Briggs JM, McCammon JA. pK(a) shift effects on backbone amide base-catalyzed hydrogen exchange rates in peptides Journal of the American Chemical Society. 120: 3735-3738. DOI: 10.1021/ja963133m  1
1997 Helms V, McCammon JA. Kinase conformations: A computational study of the effect of ligand binding Protein Science. 6: 2336-2343. PMID 9385635 DOI: 10.1002/pro.5560061106  1
1997 Radi? Z, Kirchhoff PD, Quinn DM, McCammon JA, Taylor P. Electrostatic influence on the kinetics of ligand binding to acetylcholinesterase. Distinctions between active center ligands and fasciculin. The Journal of Biological Chemistry. 272: 23265-77. PMID 9287336 DOI: 10.1074/jbc.272.37.23265  1
1997 Taylor P, Ross EM, Sternweis PC, Neubig RR, McCammon JA. Colloquium on signaling and molecular structure in pharmacology (La Jolla, California, March 11-12, 1997). Molecular Pharmacology. 52: 1-5. PMID 9224805 DOI: 10.1124/mol.52.1.1  1
1997 Allison SA, Potter M, McCammon JA. Modeling the electrophoresis of lysozyme. II. Inclusion of ion relaxation. Biophysical Journal. 73: 133-40. PMID 9199778 DOI: 10.1016/S0006-3495(97)78054-8  0.76
1997 Gilson MK, Given JA, Bush BL, McCammon JA. The statistical-thermodynamic basis for computation of binding affinities: A critical review Biophysical Journal. 72: 1047-1069. PMID 9138555 DOI: 10.1016/S0006-3495(97)78756-3  1
1997 Marrone TJ, Briggs JM, McCammon JA. Structure-based drug design: computational advances. Annual Review of Pharmacology and Toxicology. 37: 71-90. PMID 9131247 DOI: 10.1146/annurev.pharmtox.37.1.71  1
1997 Fogolari F, Elcock AH, Esposito G, Viglino P, Briggs JM, McCammon JA. Electrostatic effects in homeodomain-DNA interactions. Journal of Molecular Biology. 267: 368-81. PMID 9096232 DOI: 10.1006/jmbi.1996.0842  1
1997 Antosiewicz J, Miller MD, Krause KL, McCammon JA. Simulation of electrostatic and hydrodynamic properties of Serratia endonuclease Biopolymers. 41: 443-450. PMID 9080779 DOI: 10.1002/(SICI)1097-0282(19970405)41:4<443::AID-BIP8>3.0.CO;2-M  1
1997 Resat H, Marrone TJ, McCammon JA. Enzyme-inhibitor association thermodynamics: explicit and continuum solvent studies. Biophysical Journal. 72: 522-32. PMID 9017183 DOI: 10.1016/S0006-3495(97)78692-2  0.44
1997 Kirchhoff PD, Dutasta JP, Collet A, McCammon JA. Structural fluctuations of a cryptophane-tetramethylammonium host-guest system: A molecular dynamics simulation Journal of the American Chemical Society. 119: 8015-8022. DOI: 10.1021/ja971186d  1
1996 Briggs JM, Marrone TJ, McCammon JA. Computational science new horizons and relevance to pharmaceutical design. Trends in Cardiovascular Medicine. 6: 198-203. PMID 21232297 DOI: 10.1016/S1050-1738(96)00068-0  1
1996 McCammon JA. A speed limit for protein folding Proceedings of the National Academy of Sciences of the United States of America. 93: 11426-11427. PMID 8876151 DOI: 10.1073/pnas.93.21.11426  1
1996 Antosiewicz J, Briggs JM, McCammon JA. Orientational steering in enzyme-substrate association: ionic strength dependence of hydrodynamic torque effects. European Biophysics Journal : Ebj. 24: 137-41. PMID 8852560  1
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