Publications 2000 - 2004


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  1. Wlodek, S.T., T. Shen, J.A. McCammon. Electrostatic Steering of Substrate to Acetylcholinesterase: Analysis of Field Fluctuations. Biopolymers 53, 265-271 (2000). [PubMed]
  2. Mordasini, T.Z., J.A. McCammon. Calculations of Relative Hydration Free Energies: A Comparative Study Using Thermodynamic Integration and an Extrapolation Method Based on a Single Reference State. J. Phys. Chem. B 104, 360-367 (2000).
  3. Carlson, H.A., J.A. McCammon. Accommodating Protein Flexibility in Computational Drug Design. Mol. Pharm. 57, 213-218 (2000). [PubMed]
  4. Straatsma, T.P., M. Philippopoulos, J.A. McCammon. NWChem: Exploiting Parallelism in Molecular Simulations. Comput. Phys. Commun. 128, 377-385 (2000).
  5. Carlson, H.A., K.M. Masukawa, K. Rubins, F.D. Bushman, W.L. Jorgensen, R.D. Lins, J.M. Briggs, J.A. McCammon. Developing a Dynamic Pharmacophore Model for HIV-1 Integrase. J. Med. Chem. 43, 2100-2114 (2000). [PubMed]
  6. Brown, F.L.H., D.M. Leitner, J.A. McCammon, K.R. Wilson. Lateral Diffusion of Membrane Proteins in the Presence of Static and Dynamic Corrals - Suggestions For Appropriate Observables. Biophys. J. 78, 2257-2269 (2000). [PubMed]
  7. Weber, W., P.H. Hünenberger, J.A. McCammon. Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation. J. Phys. Chem. B 104, 3668-3675 (2000).
  8. Wriggers, W., R.K. Agrawal, D.L. Drew, J.A. McCammon, J. Frank. Domain Motions of EF-G Bound to the 70S Ribosome: Insights From a Hand-Shaking Between Multi-Resolution Structures. Biophys. J. 79, 1670-1678 (2000).
  9. Bała, P., P. Grochowski, K. Nowiński, B. Lesyng, J.A. McCammon. Quantum-Dynamical Picture of a Multi-Step Enzymatic Process. Reaction Catalyzed by Phospholipase A2. Biophys. J. 79, 1253-1262 (2000). [PubMed]
  10. Sotriffer, C.A., H. Ni, J.A. McCammon. HIV-1 Integrase Inhibitor Interactions at the Active Site: Prediction of Binding Modes Unaffected by Crystal Packing. J. Amer. Chem. Soc. 122, 6136-6137 (2000).
  11. Sotriffer, C.A., H. Ni, J.A. McCammon. Active Site Binding Modes of HIV-1 Integrase Inhibitors. J. Med. Chem. 43, 4109-4117 (2000). [PubMed]
  12. Yoo, H.-Y., J.A. Boatz, V. Helms, J.A. McCammon, P.W. Langhoff. Chromophore Protonation States and the Proton Shuttle Mechanism in Green Fluorescent Protein: Inferences Drawn from ab Initio Theoretical Studies of Structures and Infrared Absorption Spectra. J. Phys. Chem. B 105, 2850-2857 (2001).
  13. Baker, N.A., D. Sept, M.J. Holst, J.A. McCammon. The Adaptive Multilevel Finite Element Solution of the Poisson-Boltzmann Equation on Massively Parallel Computers. IBM J. Res. Devel. 45, 427-438 (2001).
  14. Straatsma, T.P., J.A. McCammon. Load Balancing of Molecular Dynamics Simulation with NWChem. IBM Systems J. 40, 328-341 (2001).
  15. Ondrechen, M.J., J.M. Briggs, J.A. McCammon. A Model for Enzyme-Substrate Interactions in Alanine Racemase. J. Amer. Chem. Soc. 123, 2830-2834 (2001). [PubMed]
  16. Elcock, A.H., J.A. McCammon. Calculation of Weak Protein-Protein Interactions: The pH Dependence of the Second Virial Coefficient. Biophys. J. 80, 613-625 (2001). [PubMed]
  17. Shen, T.Y., K. Tai, J.A. McCammon. Statistical Analysis of the Fractal Gating Motions of the Enzyme Acetylcholinesterase. Phys. Rev. E 63, article 041902 (2001). [PubMed]
  18. McCammon, J.A. Historical Overview and Future Challenges. In "Free Energy Calculations in Rational Drug Design," M.R. Reddy and M.D. Erion, Eds., Kluwer Publishing, The Netherlands, pp. 1-6 (2001).
  19. Nolen, B., C.Y. Yun, C.F. Wong, J.A. McCammon, X.-D. Fu, G. Ghosh. The X-ray Crystal Structure of an SR Protein Kinase in Yeast (Sky1p) Reveals a Novel Mechanism for Constitutive Activity. Nature Struct. Biol. 8, 176-183 (2001). [PubMed]
  20. Elcock, A.H., D. Sept, J.A. McCammon. Computer Simulation of Protein-Protein Interactions. J. Phys. Chem. B 105, 1504-1518 (2001).
  21. Elcock, A.H., J.A. McCammon. Identification of Protein Oligomerisation States by Analysis of Interface Conservation. Proc. Natl. Acad. Sci. USA 98, 2990-2994 (2001). [PubMed]
  22. Wong, C.F., P.H. Hünenberger, P. Akamine, N. Narayana, T. Diller, J.A. McCammon, S. Taylor, N.-H. Xuong. Computational Analysis of PKA-Balanol Interactions. J. Med. Chem. 44, 1530-1539 (2001). [PubMed]
  23. Tai, K., T. Shen, U. Börjesson, M. Philippopoulos, J.A. McCammon. Analysis of a Ten-nanosecond Molecular Dynamics Simulation of Mouse Acetylcholinesterase. Biophys. J. 81, 715-724 (2001). [PubMed]
  24. Sept, D., J.A. McCammon. Thermodynamics and Kinetics of Actin Filament Nucleation. Biophys. J. 81, 667-674 (2001). [PubMed]
  25. Baker, N.A., D. Sept, S. Joseph, M.J. Holst, J.A. McCammon. Electrostatics of Nanosystems: Application to Microtubules and the Ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 (2001). [PubMed]
  26. Ni, H., C.A. Sotriffer, J.A. McCammon. Ordered Water and Ligand Mobility in the HIV-1 Integrase-5CITEP Complex: A Molecular Dynamics Study. J. Med. Chem. 44, 3043-3047 (2001). [PubMed]
  27. Shen, T., C.F. Wong, J.A. McCammon. Atomistic Brownian Dynamics Simulation of Peptide Phosphorylation. J. Amer. Chem. Soc. 123, 9107-9111 (2001). [PubMed]
  28. Morikis, D., A.H. Elcock, P.A. Jennings, J.A. McCammon. Native State Conformational Dynamics of GART: A Regulatory pH-Dependent Coil-Helix Transition Examined by Electrostatic Calculations. Protein Sci. 10, 2363-2378 (2001). [PubMed]
  29. Morikis, D., A.H. Elcock, P.A. Jennings, J.A. McCammon. Proton Transfer Dynamics of GART: The pH-Dependent Catalytic Mechanism Examined by Electrostatic Calculations. Protein Sci. 10, 2379-2392 (2001). [PubMed]
  30. Andrianantoandro, E., L. Blanchoin, D. Sept, J.A. McCammon, T.D. Pollard. Kinetic Mechanism of End to End Annealing of Actin Filaments. J. Mol. Biol. 312, 721-730 (2001). [PubMed]
  31. Baker, N.A., K. Tai, R. Henchman, D. Sept, A. Elcock, M. Holst, J.A. McCammon. Mathematics and Molecular Neurobiology. In "Computational Methods for Macromolecular Modeling: Challenges and Applications," Vol. 24, Tamar Schlick and Hin Hark Gan, Eds., Springer-Verlag, pp. 31-60 (2002).
  32. Ma, C., N.A. Baker, S. Joseph, J.A. McCammon. Binding of Aminoglycoside Antibiotics to the Small Ribosomal Subunit: A Continuum Electrostatics Investigation. J. Amer. Chem. Soc. 124, 1438-1442 (2002). [PubMed]
  33. Shen, T., K. Tai, R.H. Henchman, J.A. McCammon. Molecular Dynamics of Acetylcholinesterase. Acc. Chem. Res. 35, 332-340 (2002). [PubMed]
  34. Henchman, R.H., J.A. McCammon. Extracting Hydration Sites around Proteins from Explicit Water Simulations. J. Comput. Chem. 23, 861-869 (2002). [PubMed]
  35. McCammon, J.A., P.G. Wolynes. Enlarging the Landscape: Editorial Overview. Curr. Opin. Struct. Biol. 12, 143-145 (2002).
  36. Gidofalvi, G., C.F. Wong, J.A. McCammon. Entropy Loss of Hydroxyl Groups of Balanol upon Binding to Protein Kinase A. J. Chem. Educ. 79, 1122-1126 (2002).
  37. Henchman, R.H., K. Tai, T. Shen, J.A. McCammon. Properties of Water Molecules in the Active Site Gorge of Acetylcholinesterase from Computer Simulation. Biophys. J. 82, 2671-2682 (2002). [PubMed]
  38. Tai, K., T. Shen, R.H. Henchman, Y. Bourne, P. Marchot, J.A. McCammon. Mechanism of Acetylcholinesterase Inhibition by Fasciculin: A 5-ns Molecular Dynamics Simulation. J. Amer. Chem. Soc. 124, 6153-6161 (2002). [PubMed]
  39. Lin, J.-H., A.L. Perryman, J.R. Schames, J.A. McCammon. Computational Drug Design Accommodating Receptor Flexibility: The Relaxed Complex Scheme. J. Amer. Chem. Soc. 124, 5632-5633 (2002). [PubMed]
  40. Lin, J.-H., N.A. Baker, J.A. McCammon. Bridging the Implicit and Explicit Solvent Approaches for Membrane Electrostatics. Biophys. J. 83, 1374-1379 (2002). [PubMed]
  41. Karplus, M., J.A. McCammon. Molecular Dynamics Simulations of Macromolecules: A Perspective. Nature Struct. Biol. 9, 646-652 (2002). [PubMed]
  42. Shen, T., L.S. Canino, J.A. McCammon. Unfolding Proteins under External Forces: A Solvable Model under the Self-consistent Pair Contact Probability Approximation. Phys. Rev. Letters 89, article 068103 (2002). [PubMed]
  43. Kua, J., Y. Zhang, J.A. McCammon. Studying Enzyme Binding Specificity in Acetylcholinesterase using a Combined Molecular Dynamics and Multiple Docking Approach. J. Amer. Chem. Soc. 124, 8260-8267 (2002). [PubMed]
  44. Rowley, D.C., M.S.T. Hansen, D. Rhodes, C.A. Sotriffer, H. Ni, J.A. McCammon, F.D. Bushman, W. Fenical. Thalassiolins A-C: New Marine-derived Inhibitors of HIV cDNA Integrase. Bioorg. Med. Chem. 10, 3619-3625 (2002). [PubMed]
  45. Henchman, R.H., J.A. McCammon. Structural and Dynamical Properties of Water Around Acetylcholinesterase. Protein Sci. 11, 2080-2090 (2002). [PubMed]
  46. Zhang, Y., J. Kua, J.A. McCammon. Role of the Catalytic Triad and Oxyanion Hole in Acetylcholinesterase Catalysis: An ab inito QM/MM Study. J. Amer. Chem. Soc. 124, 10572-10577 (2002). [PubMed]
  47. Perryman, A.L., J.A. McCammon. AutoDocking Dinucleotides to the HIV-1 Integrase Core Domain: Exploring Possible Binding Sites for Viral and Genomic DNA. J. Med. Chem. 45, 5624-5627 (2002). [PubMed]
  48. Canino, L.S., T. Shen, J.A. McCammon. Changes in Flexibility Upon Binding: Application of the Self-Consistent Pair Contact Probability Method to Protein-Protein Interactions. J. Chem. Phys. 117, 9927-9933 (2002).
  49. Lin, J.-H., A.L. Perryman, J.R. Schames, J.A. McCammon. The Relaxed Complex Method: Accommodating Receptor Flexibility for Drug Design with an Improved Scoring Scheme. Biopolymers 68, 47-62 (2003, Kollman memorial issue). [PubMed]
  50. Podtelezhnikov, A.A., K. Gao, F.D. Bushman, J.A. McCammon. Modeling HIV-1 Integrase Complexes Based on their Hydrodynamic Properties. Biopolymers 68, 110-120 (2003, Kollman memorial issue). [PubMed]
  51. Baker, N.A., J.A. McCammon. Electrostatic Interactions. In "Structural Bioinformatics," H. Weissig and P.E. Bourne, Eds., John Wiley & Sons, New York, pp. 427-440 (2003). [PubMed]
  52. Wong, C.F., J.A. McCammon. Protein Flexibility and Computer-aided Drug Design. Ann. Rev. Pharmacol. Toxicol. 43, 31-45 (2003). [PubMed]
  53. Nielsen, J.E., J.A. McCammon. On the Evaluation and Optimisation of Protein X-ray Structures for pKa Calculations. Protein Sci. 12, 313-326 (2003). [PubMed]
  54. Zhang, Y., J.A. McCammon. Studying the Affinity and Kinetics of Molecular Association with Molecular Dynamics Simulation. J. Chem. Phys. 118, 1821-1827 (2003).
  55. Wong, C.F., J.A. McCammon. Protein Simulation and Drug Design. Adv. Protein Chem. 66, 87-121 (2003).
  56. Morikis, D., A.H. Elcock, P.A. Jennings, J.A. McCammon. The pH Dependence of Stability of the Activation Helix and the Catalytic site of GART. Biophys. Chem. 105, 279-291 (2003). [PubMed]
  57. Shen, T., C.F. Wong, J.A. McCammon. Brownian Dynamics Simulation of Helix-Capping Motifs. Biopolymers 70, 252-259 (2003). [PubMed]
  58. Tøndel, K., C.F. Wong, J.A. McCammon. Computational Analysis of the Interactions between the Angiogenesis Inhibitor PD173074 and Fibroblast Growth Factor Receptor 1. J. Theor. Comput. Chem. 2, 43-56 (2003).
  59. Tai, K., S.D. Bond, H.R. MacMillan, N.A. Baker, M.J. Holst, J.A. McCammon. Finite Element Simulations of Acetylcholine Diffusion in Neuromuscular Junctions. Biophys. J. 84, 2234-2241 (2003). [PubMed]
  60. Zhang, Y., J. Kua, J.A. McCammon. Influence of Structural Fluctuation on Enzyme Reaction Energy Barriers in Combined Quantum Mechanical/Molecular Mechanical Studies. J. Phys. Chem. B 107, 4459-4463 (2003).
  61. Sims, P.A., C.F. Wong, J.A. McCammon. A Computational Model of Binding Thermodynamics: The Design of Cyclin-dependent Kinase 2 Inhibitors. J. Med. Chem. 46, 3314-3325 (2003). [PubMed]
  62. Shi, J., K. Tai, J.A. McCammon, P. Taylor, D.A. Johnson. Nanosecond Dynamics of the Mouse Acetylcholinesterase Cys69-Cys96 Omega Loop. J. Biol. Chem. 278, 30905-30911 (2003). [PubMed]
  63. Puerta, D.T., J.R. Schames, R.H. Henchman, J.A. McCammon, S.M. Cohen. From Model Complexes to Metalloprotein Inhibition: A Synergistic Approach to Structure-based Drug Discovery. Angew. Chem. Int. Ed. 42, 3772-3774 (2003). [PubMed]
  64. Nielsen, J.E., J.A. McCammon. Calculating pKa Values in Enzyme Active Sites. Protein Sci. 12, 1894-1901 (2003). [PubMed]
  65. Cerutti, D.S., C.F. Wong, J.A. McCammon. Brownian Dynamics Simulations of Ion Atmospheres around Polyalanine and B-DNA: Effects of Biomolecular Dielectric. Biopolymers 70, 391-402 (2003). [PubMed]
  66. Sept, D., N.A. Baker, J.A. McCammon. The Physical Basis of Microtubule Structure and Stability. Protein Sci. 12, 2257-2261 (2003). [PubMed]
  67. Bui, J.M., R.H. Henchman, J.A. McCammon. The Dynamics of Ligand Barrier Crossing inside the Acetylcholinesterase Gorge. Biophys. J. 85, 2267-2272 (2003). [PubMed]
  68. Henchman, R.H., H.-L. Wang, S.M. Sine, P. Taylor, J.A. McCammon. Asymmetric Structural Motions of the Homomeric α7 Nicotinic Receptor Ligand Binding Domain Revealed by Molecular Dynamics Simulation. Biophys. J. 85, 3007-3018 (2003). [PubMed]
  69. Kua, J., Y. Zhang, A.C. Eslami, J.R. Butler, J.A. McCammon. Studying the roles of W86, E202, and Y337 in binding of acetylcholine to acetylcholinesterase using a combined molecular dynamics and multiple docking approach. Protein Sci. 12, 2675-2684 (2003). [PubMed]
  70. Vitalis, A., N.A. Baker, J.A. McCammon. ISIM: A Program for Grand Canonical Monte Carlo Simulations of the Ionic Environment of Biomolecules. Mol. Sim. 30, 45-61 (2004).
  71. Tai, K., T. Shen, R.H. Henchman, Y. Bourne, P. Marchot, J.A. McCammon. Mechanism of Acetylcholinesterase Inhibition by Fasciculin: A 5 ns Molecular Dynamics Simulation. In "Cholinergic Mechanisms," I. Silman, H. Soreq, L. Anglister, D.M. Michaelson, and A. Fisher, Eds., Taylor & Francis, Ch. 141, pp. 727-728 (2004).
  72. Henchman, R., K. Tai, T. Shen, J.A. McCammon. Influence of Water on the Function of Acetylcholinesterase. In "Cholinergic Mechanisms," I. Silman, H. Soreq, L. Anglister, D.M. Michaelson, and A. Fisher, Eds., Taylor & Francis, Ch. 98, pp. 589-590 (2004).
  73. Bui, J., J.A. McCammon. The Displacement of Ligand through the Bottleneck Region of the Acetylcholinesterase Gorge. In "Cholinesterases in the Second Millennium: Biomolecular and Pathological Aspects," N.C. Inestrosa and E.O. Campos, Eds., pp. 207-211 (2004).
  74. Wong, C.F., J.A. McCammon. Drug Design. In "Encyclopedia of Supramolecular Chemistry," J. Atwood and J. Steed, Eds., Marcel Dekker, NY, pp. 490-496 (2004).
  75. Swanson, J.M.J., R.H. Henchman, J.A. McCammon. Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free Energy. Biophys. J. 86, 67-74 (2004). [PubMed]
  76. Trylska, J., P. Grochowski, J.A. McCammon. The Role of Hydrogen Bonding in the Enzymatic Reaction Catalyzed by HIV-1 Protease. Protein Sci. 13, 513-528 (2004). [PubMed]
  77. Song, Y., Y. Zhang, T. Shen, C.L. Bajaj, J.A. McCammon, N.A. Baker. Finite Element Solution of the Steady-state Smoluchowski Equation for Rate Constant Calculations. Biophys. J. 86, 2017-2029 (2004). [PubMed]
  78. Perryman, A.L., J.-H. Lin, J.A. McCammon. HIV-1 Protease Molecular Dynamics of a Wild-Type and of the V82F/I84V Mutant: Possible Contributions to Drug Resistance and a Potential New Target Site for Drugs. Protein Sci. 13, 1108-1123 (2004). [PubMed]
  79. Schames, J.R., R.H. Henchman, J.S. Siegel, C.A. Sotriffer, H. Ni, J.A. McCammon. Discovery of a Novel Binding Trench in HIV Integrase. J. Med. Chem. 47, 1879-1881 (2004). [PubMed]
  80. Trylska, J., R. Konecny, F. Tama, C.L. Brooks III, J.A. McCammon. Ribosome Motions Modulate Electrostatic Properties. Biopolymers 74, 423-431 (2004). [PubMed]
  81. Dolinsky, T.J., J.E. Nielsen, J.A. McCammon, N.A. Baker. PDB2PQR: An Automated Pipeline for the Setup, Execution and Analysis of Poisson-Boltzmann Electrostatics Calculations. Nucleic Acids Res. 32, W665-W667 (2004). [PubMed]
  82. Hamelberg, D., J. Mongan, J.A. McCammon. Accelerated Molecular Dynamics: A Promising and Efficient Simulation Method for Biomolecules. J. Chem. Phys. 120, 11919-11929 (2004). [PubMed]
  83. Bui, J.M., K. Tai, J.A. McCammon. Acetylcholinesterase: Enhanced Fluctuations and Alternative Routes to the Active Site in the Complex with Fasciculin-2. J. Amer. Chem. Soc. 126, 7198-7205 (2004). [PubMed]
  84. Sims, P.A., C.F. Wong, J.A. McCammon. Charge Optimization of the Interface between Protein Kinases and their Ligands. J. Comput. Chem. 25, 1416-1429 (2004). [PubMed]
  85. Hamelberg, D., J.A. McCammon. Standard Free Energy of Releasing a Localized Water Molecule from the Binding Pockets of Proteins: Double-Decoupling Method. J. Amer. Chem. Soc. 126, 7683-7689 (2004). [PubMed]
  86. Zhang, D., R. Konecny, N.A. Baker, J.A. McCammon. Electrostatic Interaction between RNA and Protein Capsid in CCMV Simulated by a Coarse-grain RNA model and a Monte Carlo Approach. Biopolymers 75, 325-337 (2004). [PubMed]
  87. Senapati, S., C.F. Wong, J.A. McCammon. Finite concentration effects on diffusion-controlled reactions. J. Chem. Phys. 121, 7896-7900 (2004). [PubMed]
  88. Mongan, J., D.A. Case, J.A. McCammon. Constant pH Molecular Dynamics in Generalized Born Implicit Solvent. J. Comput. Chem. 25, 2038-2048 (2004). [PubMed]

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