Publications 1995 - 1999

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  1. Luty, B.A., Z.R. Wasserman, P.F.W. Stouten, C.N. Hodge, M. Zacharias, J.A. McCammon. A Molecular Mechanics/Grid Method for Evaluation of Ligand-Receptor Interactions. J. Comput. Chem. 16, 454-464 (1995).
  2. Cannon, W.R., J.M. Briggs, J. Shen, J.A. McCammon, F.A. Quiocho. Conservative and Nonconservative Mutations in Proteins: Anomalous Mutations in a Transport Receptor Analyzed by Free Energy and Quantum Chemical Calculations. Protein Sci. 4, 387-393 (1995). [PubMed]
  3. Wlodek, S.T., J. Antosiewicz, J.A. McCammon, M.K. Gilson. Binding of Cations and Protons in the Active Site of Acetylcholinesterase. In "Modelling of Biomolecular Structures and Mechanisms," Vol. 27, A. Pullman, J. Jortner, and B. Pullman, Eds., Kluwer Academic Pub., pp. 25-37 (1995).
  4. Antosiewicz, J., M.K. Gilson, I.H. Lee, J.A. McCammon. Acetylcholinesterase: Diffusional Encounter Rate Constants for Dumbbell Models of Ligand. Biophys. J. 68, 62-68 (1995). [PubMed]
  5. Ilin, A., B. Bagheri, L.R. Scott, J.M. Briggs, J.A. McCammon. Parallelization of Poisson-Boltzmann and Brownian Dynamics Calculations. Amer. Chem. Soc. Sympos. Series, No. 592, 170-185 (1995).
  6. Bała, P., P. Grochowski, B. Lesyng, J.A. McCammon. Quantum-Classical Molecular Dynamics and Its Computer Implementation. Comput. & Chem. 19, 155-160 (1995).
  7. Soman, K.V., J.A. McCammon, A.M. Brown. Secondary Structure Prediction of the H5-Pore of Potassium Channels. Protein Eng. 8, 397-401 (1995). [PubMed]
  8. Gilson, M.K., J.A. McCammon, J.D. Madura. Molecular Dynamics Simulation with a Continuum Electrostatic Model of the Solvent. J. Comput. Chem. 16, 1081-1095 (1995).
  9. Antosiewicz, J., J.A. McCammon, S.T. Wlodek, M.K. Gilson. Simulation of Charge-Mutant Acetylcholinesterases. Biochemistry 34, 4211-4219 (1995). [PubMed]
  10. Pomés, R., R.C. Willson, J.A. McCammon. Free Energy Simulations of the HyHEL-10/HEL Antibody-Antigen Complex. Protein Eng. 8, 663-675 (1995). [PubMed]
  11. Madura, J.D., J.M. Briggs, R.C. Wade, M.E. Davis, B.A. Luty, A. Ilin, J. Antosiewicz, M.K. Gilson, B. Bagheri, L.R. Scott, J.A. McCammon. Electrostatics and Diffusion of Molecules in Solution: Simulations with the University of Houston Brownian Dynamics Program. Comput. Phys. Commun. 91, 57-95 (1995).
  12. Wlodek, S.T., J. Antosiewicz, M.K. Gilson, J.A. McCammon, T.W. Clark, L.R. Scott. Computer Modeling of Acetylcholinesterase and Acetylcholinesterase-Ligand Complexes. In "Enzymes of the Cholinesterase Family," D.M. Quinn, et al., Eds., Plenum, pp. 97-104 (1995).
  13. McDonald, S.M., R.C. Willson, J.A. McCammon. Determination of the pKa Values of Titratable Groups of an Antigen-Antibody Complex: HyHEL5-HEL. Protein Eng. 8, 915-924 (1995). [PubMed]
  14. Antosiewicz, J., J.A. McCammon. Electrostatic and Hydrodynamic Orientational Steering Effects in Enzyme-Substrate Association. Biophys. J. 69, 57-65 (1995). [PubMed]
  15. Clark, T.W., L.R. Scott, S. Wlodek, J.A. McCammon. I/O Limitations in Parallel Molecular Dynamics. In "Proceedings of the 1995 ACM/IEEE Supercomputing Conference," F. Baker and J. Wehmer, Eds., IEEE Computer Society Press, pp. 1-15 (1995, refereed).
  16. Elcock, A.H., J.A. McCammon. Sequence Dependent Hydration of DNA: Theoretical Results. J. Amer. Chem. Soc. 117, 10161-10162 (1995).
  17. Bała, P., P. Grochowski, B. Lesyng, J.A. McCammon. Quantum Mechanical Simulation Methods for Studying Biological Systems. Les Houches Physics Schools Series, Springer Verlag, Berlin, pp. 119-156 (1995).
  18. Elcock, A.H., J.A. McCammon. The Low Dielectric Interior of Proteins is Sufficient to Cause Major Structural Changes in DNA on Association. J. Amer. Chem. Soc. 118, 3787-3788 (1996).
  19. Kirchhoff, P.D., M.B. Bass, B.A. Hanks, J.M. Briggs, A. Collet, J.A. McCammon. Structural Fluctuations of a Cryptophane Host: A Molecular Dynamics Simulation. J. Amer. Chem. Soc. 118, 3237-3246 (1996).
  20. Smart, J.L., J.A. McCammon. Surface Titration: A Continuum Electrostatics Model. J. Amer. Chem. Soc. 118, 2283-2284 (1996).
  21. Potter, M.J., B. Luty, H.-X. Zhou, J.A. McCammon. Time-Dependent Rate Coefficients from Brownian Dynamics Simulations. J. Phys. Chem. 100, 5149-5154 (1996).
  22. Resat, H., J.A. McCammon. Free Energy Simulations: Correcting for Electrostatic Cutoffs by Use of the Poisson Equation. J. Chem. Phys. 104, 7645-7651 (1996).
  23. Antosiewicz, J., J.A. McCammon, M.K. Gilson. The Determinants of pKas in Proteins. Biochemistry 35, 7819-7833 (1996). [PubMed]
  24. Bała, P., P. Grochowski, B. Lesyng, J.A. McCammon. Quantum-Classical Molecular Dynamics Simulations of Proton Transfer Processes in Molecular Complexes and in Enzymes. J. Phys. Chem. 100, 2535-2545 (1996).
  25. Antosiewicz, J., J.M. Briggs, J.A. McCammon. Orientational Steering in Enzyme-Substrate Association: Ionic Strength Dependence of Hydrodynamic Torque Effects. Euro. Biophys. J. 24, 137-141 (1996). [PubMed]
  26. Marrone, T.J., M.K. Gilson, J.A. McCammon. Comparison of Continuum and Explicit Models of Solvation: Potentials of Mean Force for Alanine Dipeptide. J. Phys. Chem. 100, 1439-1441 (1996).
  27. Wlodek, S.T., J. Antosiewicz, J.A. McCammon, T.P. Straatsma, M.K. Gilson, J.M. Briggs, C. Humblet, J.L. Sussman. Binding of Tacrine and 6-Chlorotacrine by Acetylcholinesterase. Biopolymers 38, 109-117 (1996). [PubMed]
  28. Resat, H., M. Mezei, J.A. McCammon. Use of the Grand Canonical Ensemble in Potential of Mean Force Calculations. J. Phys. Chem. 100, 1426-1433 (1996).
  29. Elamrani, S., M.B. Berry, G.N. Phillips, Jr., J.A. McCammon. Study of Global Motions in Proteins by Weighted Masses Molecular Dynamics: Adenylate Kinase as a Test Case. Proteins 25, 79-88 (1996). [PubMed]
  30. Marrone, T.J., T.P. Straatsma, J.M. Briggs, D.K. Wilson, F.A. Quiocho, J.A. McCammon. Theoretical Study of Inhibition of Adenosine Deaminase by 8R-Coformycin and 8R-Deoxycoformycin. J. Med. Chem. 39, 277-284 (1996). [PubMed]
  31. Grochowski, P., B. Lesyng, P. Bała, J.A. McCammon. Density Functional Based Parametrization of a Valence Bond Method and its Applications in Quantum-Classical Molecular Dynamics Simulations of Enzymatic Reactions. Int. J. Quant. Chem. 60, 1143-1164 (1996).
  32. Elcock, A.H., M.J. Potter, D.A. Matthews, D.R. Knighton, J.A. McCammon. Electrostatic Channeling in the Bifunctional Enzyme Dihydrofolate Reductase-Thymidylate Synthase. J. Mol. Biol. 262, 370-374 (1996). [PubMed]
  33. Briggs, J.M., T.J. Marrone, J.A. McCammon. Computational Science: New Horizons and Relevance to Pharmaceutical Design. Trends Cardiovasc. Med. 6, 198-204 (1996). [PubMed]
  34. McCammon, J.A. A Speed Limit for Protein Folding (Commentary). Proc. Natl. Acad. Sci. USA 93, 11426-11427 (1996). [PubMed]
  35. Elcock, A.H., J.A. McCammon. Evidence for Electrostatic Channeling in a Fusion Protein of Malate Dehydrogenase and Citrate Synthase. Biochemistry 35, 12652-12658 (1996). [PubMed]
  36. Antosiewicz, J., S.T. Wlodek, J.A. McCammon. Acetylcholinesterase: Role of the Enzyme's Charge Distribution in Steering Charged Ligands Toward the Active Site. Biopolymers 39, 85-94 (1996). [PubMed]
  37. Antosiewicz, J., J.M. Briggs, A.H. Elcock, M.K. Gilson, J.A. McCammon. Computing the Ionization States of Proteins with a Detailed Charge Model. J. Comput. Chem. 17, 1633-1644 (1996).
  38. Zhou, H.-X., J.M. Briggs, J.A. McCammon. A 240-Fold Electrostatic Rate-Enhancement for Acetylcholinesterase - Substrate Binding can be Predicted by the Potential within the Active Site. J. Amer. Chem. Soc. 118, 13069-13070 (1996).
  39. Costante-Crassous, J., T.J. Marrone, J.M. Briggs, J.A. McCammon, A. Collet. Absolute Configuration of Bromochlorofluoromethane from Molecular Dynamics Simulation of its Enantioselective Complexation by Cryptophane-C. J. Amer. Chem. Soc. 119, 3818-3823 (1997).
  40. Antosiewicz, J., M.D. Miller, K.L. Krause, J.A. McCammon. Simulation of Electrostatic and Hydrodynamic Properties of Serratia Endonuclease. Biopolymers 41, 443-450 (1997). [PubMed]
  41. Marrone, T.J., J.M. Briggs, J.A. McCammon. Structure-Based Drug Design: Computational Advances. Ann. Rev. Pharmacol. Toxicol. 37, 71-90 (1997). [PubMed]
  42. Elcock, A.H., M.J. Potter, J.A. McCammon. Application of Poisson-Boltzmann Solvation Forces to Macromolecular Simulations. In "Computer Simulation of Biomolecular Systems," Vol. 3, W.F. van Gunsteren, P.K. Weiner, and A.J. Wilkinson, Eds., Kluwer Academic Publishers, Dordrecht, pp. 244-261 (1997).
  43. Resat, H., T.J. Marrone, J.A. McCammon. Enzyme-Inhibitor Association Thermodynamics: Explicit and Continuum Solvent Studies. Biophys. J. 72, 522-532 (1997). [PubMed]
  44. Fogolari, F., A.H. Elcock, G. Esposito, P. Viglino, J.M. Briggs, J.A. McCammon. Electrostatic effects in homeodomain-DNA interactions. J. Mol. Biol. 267, 368-381 (1997). [PubMed]
  45. Wlodek, S.T., J. Antosiewicz, J.A. McCammon. Prediction of Titration Properties of Structures of a Protein Derived from Molecular Dynamics Trajectories. Protein Sci. 6, 373-382 (1997). [PubMed]
  46. Gilson, M.K., J.A. Given, B.L. Bush, J.A. McCammon. The Statistical-Thermodynamic Basis for Computation of Binding Affinities: A Critical Review. Biophys. J. 72, 1047-1069 (1997). [PubMed]
  47. Hodge, C.N., T.P. Straatsma, J.A. McCammon, A. Wlodawer. Rational Design of HIV Protease Inhibitors. In "Structural Biology of Viruses," W. Chiu, R.M. Burnett, and R. Garcea, Eds., Oxford University Press, pp. 451-473 (1997).
  48. Huber, G.A., J.A. McCammon. Weighted-Ensemble Simulated Annealing: Faster Optimization on Hierarchical Energy Surfaces. Phys. Rev. E 55, 4822-4825 (1997).
  49. Smart, J.L., T.J. Marrone, J.A. McCammon. Conformational Sampling with Poisson-Boltzmann Forces and a Stochastic Dynamics/Monte Carlo Method: Application to Alanine Dipeptide. J. Comput. Chem. 18, 1750-1759 (1997).
  50. Allison, S.A., M. Potter, J.A. McCammon. Modeling the Electrophoresis of Lysozyme II. Inclusion of Ion Relaxation. Biophys. J. 73, 133-140 (1997). [PubMed]
  51. Taylor, P., E.M. Ross, P.C. Sternweis, R. Neubig, J.A. McCammon. Colloquium on Signaling and Molecular Structure in Pharmacology. Mol. Pharm. 52, 1-5 (1997). [PubMed]
  52. Kirchhoff, P.D., J.-P. Dutasta, A. Collet, J.A. McCammon. Structural Fluctuations of a Cryptophane-Tetramethylammonium Host-Guest System: A Molecular Dynamics Simulation. J. Amer. Chem. Soc. 119, 8015-8022 (1997).
  53. Radić, Z., P.D. Kirchhoff, D.M. Quinn, J.A. McCammon, P. Taylor. Electrostatic Influence on the Kinetics of Ligand Binding to Acetylcholinesterase: Distinctions Between Active Center Ligands and Fasciculin. J. Biol. Chem. 272, 23265-23277 (1997). [PubMed]
  54. Baginski, M., H. Resat, J.A. McCammon. Molecular Properties of Amphotericin B Membrane Channel - A Molecular Dynamics Simulation. Mol. Pharm. 52, 560-570 (1997). [PubMed]
  55. Wlodek, S.T., T.W. Clark, L.R. Scott, J.A. McCammon. Molecular Dynamics of Acetylcholinesterase Dimer Complexed with Tacrine. J. Amer. Chem. Soc. 119, 9513-9522 (1997).
  56. Helms, V., J.A. McCammon. Kinase Conformations: A Computational Study of the Effect of Ligand Binding. Protein Sci. 6, 2336-2343 (1997). [PubMed]
  57. Elcock, A.H., J.A. McCammon. A Continuum Solvation Model for Studying Protein Hydration Thermodynamics at High Temperatures. J. Phys. Chem. B 101, 9624-9634 (1997).
  58. Gibas, C.J., S. Subramaniam, J.A. McCammon, B.C. Braden, R.J. Poljak. pH Dependence of Antibody/Lysozyme Complexation. Biochemistry 36, 15599-15614 (1997). [PubMed]
  59. Elcock, A.H., G.A. Huber, J.A. McCammon. Electrostatic Channeling of Substrates Between Enzyme Active Sites: Comparison of Simulation and Experiment. Biochemistry 36, 16049-16058 (1997). [PubMed]
  60. Bała, P., T. Clark, P. Grochowski, B. Lesyng, J.A. McCammon. Parallel Version of the Combined Quantum Classical Molecular Dynamics Code for Complex Molecular and Biomolecular Systems. In "Recent Advances in Parallel Virtual Machine and Message Passing Interface," M. Bubak, J. Dongarra, and J. Wasniewski, Eds., (Lecture Notes in Computer Science 1332), Springer-Verlag Berlin-Heidelberg, pp. 409-416 (1997).
  61. Bała, P., P. Grochowski, B. Lesyng, J.A. McCammon. Quantum Classical Molecular Dynamics Simulation of Phospholipid Hydrolysis. HyperNews 2, 18-21 (1997).
  62. McCammon, J.A. Computer-Aided Structure-Based Drug Discovery. In "Rational Molecular Design in Drug Research," Alfred Benzon Symposium 42, T. Liljefors, F.S. Jorgensen, and P. Krogsgaard-Larsen, Eds., Munksgaard, Copenhagen, pp. 189-196 (1998).
  63. Fogolari, F., G. Esposito, P. Viglino, J.M. Briggs, J.A. McCammon. pKa Shift Effects on Backbone Amide Base-Catalyzed Hydrogen Exchange Rates in Peptides. J. Amer. Chem. Soc. 120, 3735-3738 (1998).
  64. Zhou, H.-X., J.M. Briggs, S. Tara, J.A. McCammon. Correlation Between Rate of Enzyme-Substrate Diffusional Encounter and Average Boltzmann Factor Around Active Site. Biopolymers 45, 355-360 (1998). [PubMed]
  65. Marrone, T.J., H. Resat, C.N. Hodge, C.-H. Chang, J.A. McCammon. Solvation Studies of DMP323 and A76928 Bound to HIV Protease: Analysis of Water Sites Using Grand Canonical Monte Carlo Simulations. Protein Sci. 7, 573-579 (1998). [PubMed]
  66. Bała, P., P. Grochowski, B. Lesyng, J.A. McCammon. Quantum Dynamics of Proton Transfer Processes in Enzymatic Reactions. Simulations of Phospholipase A2. Ber. Bunsenges. Phys. Chem. 120, 580-586 (1998).
  67. McCammon, J.A. Theory of Biomolecular Recognition. Curr. Opin. Struct. Biol. 8, 245-249 (1998). [PubMed]
  68. Resat, H., J.A. McCammon. Correcting for Electrostatic Cutoffs in Free Energy Simulations: Toward Consistency Between Simulations with Different Cutoffs. J. Chem. Phys. 108, 9617-9623 (1998).
  69. Elcock, A.H., J.A. McCammon. Electrostatic Contributions to the Stability of Halophilic Proteins. J. Mol. Biol. 280, 731-748 (1998). [PubMed]
  70. Smart, J.L., J.A. McCammon. Analysis of Synaptic Transmission in the Neuromuscular Junction Using a Continuum Finite Element Model. Biophys. J. 75, 1679-1688 (1998). [PubMed]
  71. Zhou, H.-X., S.T. Wlodek, J.A. McCammon. Conformation Gating as a Mechanism for Enzyme Specificity. Proc. Natl. Acad. Sci. USA 95, 9280-9283 (1998). [PubMed]
  72. Tara, S., A.H. Elcock, P.D. Kirchhoff, J.M. Briggs, Z. Radić, P. Taylor, J.A. McCammon. 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, 465-474 (1998). [PubMed]
  73. Bała, P., T. Clark, P. Grochowski, B. Lesyng, K. Nowinski, J.A. McCammon. Advanced Calculations and Visualization of Enzymatic Reactions with the Combined Quantum Classical Molecular Dynamics Code. In "Recent Advances in Applied Parallel Computing," B. Kagstrom, J. Dongarra, E. Elmroth, and J. Wasniewski, Eds., (Lecture Notes in Computer Science 1541), Springer-Verlag Berlin-Heidelberg, pp. 20-27 (1998).
  74. Wriggers, W., R.A. Milligan, K. Schulten, J.A. McCammon. Self-Organizing Neural Networks Bridge the Biomolecular Resolution Gap. J. Mol. Biol. 284, 1247-1254 (1998). [PubMed]
  75. Helms, V., E.F.Y. Hom, T.P. Straatsma, J.A. McCammon, P. Langhoff. Exciting Green Fluorescent Protein. In "Combined Quantum Mechanical and Molecular Mechanical Methods," J. Gao and M.A. Thompson, Eds., ACS Symposium Series 712, American Chemical Society, Washington, DC, pp. 288-295 (1998).
  76. Weber, W., H. Demirdjian, R.D. Lins, J.M. Briggs, R. Ferreira, J.A. McCammon. Brownian and Essential Dynamics Studies of the HIV-1 Integrase Catalytic Domain. J. Biomol. Struct. Dyn. 16, 733-745 (1998). [PubMed]
  77. McCammon, J.A., S. Wlodek, T. Clark, P. Kirchhoff, L.R. Scott, S. Tara. Computer Simulation Studies of Acetylcholinesterase Dynamics and Activity. In "Structure and Function of Cholinesterases and Related Proteins," B.P. Doctor, P. Taylor, D.M. Quinn, R.L. Rotundo, and M.K. Gentry, Eds., Plenum Press, New York, pp. 327-329 (1998).
  78. Antosiewicz, J., E. Błachut-Okrasińska, T. Grycuk, J.M. Briggs, S.T. Wlodek, B. Lesyng, J.A. McCammon. Prediction of pKas of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute-Solvent System. In "Computational Molecular Dynamics: Challenges, Methods, Ideas," P. Deuflhard, J. Hermans, B. Leimkuhler, A.E. Mark, S. Reich, and R.D. Skeel, Eds., Springer, Berlin, pp. 176-196 (1999).
  79. McCammon, J.A. Are Molecular Motions Important for Function? In "Simplicity and Complexity in Proteins and Nucleic Acids," Vol. 83, H. Frauenfelder, J. Deisenhofer, and P.G. Wolynes, Eds., Berlin: Dahlem University Press, pp. 193-198 (1999).
  80. Dill, K.A., J. Deisenhofer, G.R. Fleming, H. Frauenfelder, K. Gerwert, J.A. McCammon, H. Michel. What Do We Need to Know about Proteins and Nucleic Acids? In "Simplicity and Complexity in Proteins and Nucleic Acids," H. Frauenfelder, J. Deisenhofer, and P.G. Wolynes, Eds., Berlin: Dahlem University Press, pp. 81-106 (1999).
  81. Helms, V., J.A. McCammon. Conformational Transitions of Proteins from Atomistic Simulations. In "Computational Molecular Dynamics: Challenges, Methods, Ideas," P. Deuflhard, J. Hermans, B. Leimkuhler, A.E. Mark, S. Reich, and R.D. Skeel, Eds., Springer, Berlin, pp. 66-77 (1999).
  82. Hünenberger, P.H., J.A. McCammon. Ewald Artifacts in Computer Simulations of Ionic Solvation and Ion-Ion Interaction: A Continuum Electrostatics Study. J. Chem. Phys. 110, 1856-1872 (1999).
  83. Carlson, H.A., J.M. Briggs, J.A. McCammon. Calculation of the pKa Values for the Ligands and Side Chains of Escherichia coli D-Alanine:D-Alanine Ligase. J. Med. Chem. 42, 109-117 (1999). [PubMed]
  84. Smart, J.L., J.A. McCammon. Phosphorylation Stabilizes the N-Termini of α-Helices. Biopolymers 49, 225-233 (1999). [PubMed]
  85. Hünenberger, P.H., V. Helms, N. Narayana, S.S. Taylor, J.A. McCammon. Determinants of Ligand Binding to cAMP-Dependent Protein Kinase. Biochemistry 38, 2358-2366 (1999). [PubMed]
  86. de Bakker, P.I.W., P.H. Hünenberger, J.A. McCammon. Molecular Dynamics Simulations of the Hyperthermophilic Protein Sac7d from Sulfolobus acidocaldarius: Contribution of Salt Bridges to Thermostability. J. Mol. Biol. 285, 1811-1830 (1999). [PubMed]
  87. Kirchhoff, P.D., J.-P. Dutasta, A. Collet, J.A. McCammon. Dynamic and Rotational Analysis of Cryptophane Host-Guest Systems: Challenges of Describing Molecular Recognition. J. Amer. Chem. Soc. 121, 381-390 (1999).
  88. Tara, S., T.P. Straatsma, J.A. McCammon. Mouse Acetylcholinesterase Unliganded and in Complex with Huperzine A: A Comparison of Molecular Dynamics Simulations. Biopolymers 50, 35-43 (1999). [PubMed]
  89. Huber, G.A., J.A. McCammon. OOMPAA - Object-Oriented Model for Probing Assemblages of Atoms. J. Comput. Phys. 151, 264-282 (1999).
  90. Xavier, K.A., S.M. McDonald, J.A. McCammon, R.C. Willson. Association and Dissociation Kinetics of Bobwhite Quail Lysozyme with Monoclonal Antibody HyHEL-5. Protein Eng. 12, 79-83 (1999). [PubMed]
  91. Wriggers, W., R.A. Milligan, J.A. McCammon. Situs: A Package for Docking Crystal Structures into Low-Resolution Maps from Electron Microscopy. J. Struct. Biol. 125, 185-195 (1999). [PubMed]
  92. Baker, N.A., J.A. McCammon. Non-Boltzmann Rate Distributions in Stochastically Gated Reactions. J. Phys. Chem. B 103, 615-617 (1999).
  93. Helms, V., T.P. Straatsma, J.A. McCammon. Internal Dynamics of Green Fluorescent Protein. J. Phys. Chem. B 103, 3263-3269 (1999).
  94. Hünenberger, P.H., J.A. McCammon. Effect of Artificial Periodicity in Simulations of Biomolecules under Ewald Boundary Conditions: A Continuum Electrostatics Study. Biophys. Chem. 78, 69-88 (1999). [PubMed]
  95. Lins, R.D., J.M. Briggs, T.P. Straatsma, H.A. Carlson, J. Greenwald, S. Choe, J.A. McCammon. Molecular Dynamics Studies on the HIV-1 Integrase Catalytic Domain. Biophys. J. 76, 2999-3011 (1999). [PubMed]
  96. Baker, N.A., P.H. Hünenberger, J.A. McCammon. Polarization Around an Ion in a Dielectric Continuum with Truncated Electrostatic Interactions. J. Chem. Phys. 110, 10679-10692 (1999).
  97. Weber, W., V. Helms, J.A. McCammon, P.W. Langhoff. Shedding Light on the Dark and Weakly Fluorescent States of Green Fluorescent Proteins. Proc. Natl. Acad. Sci. USA 96, 6177-6182 (1999). [PubMed]
  98. Tara, S., V. Helms, T.P. Straatsma, J.A. McCammon. Molecular Dynamics of Mouse Acetylcholinesterase Complexed with Huperzine A. Biopolymers 50, 347-359 (1999). [PubMed]
  99. Baker, N.A., V. Helms, J.A. McCammon. Dynamical Properties of Fasciculin-2. Proteins: Str. Fn. Gen. 36, 447-453 (1999). [PubMed]
  100. Potter, M.J., P.D. Kirchhoff, H.A. Carlson, J.A. McCammon. Molecular Dynamics of Cryptophane and its Complexes with Tetramethylammonium and Neopentane Using a Continuum Solvent Model. J. Comput. Chem. 20, 956-970 (1999).
  101. Błachut-Okrasińska, E., B. Lesyng, J.M. Briggs, J.A. McCammon, J.M. Antosiewicz. Poisson-Boltzmann Model Studies of Molecular Electrostatic Properties of the cAMP-Dependent Protein Kinase. Euro. Biophys. J. 28, 457-467 (1999). [PubMed]
  102. Elcock, A.H., R.R. Gabdoulline, R.C. Wade, J.A. McCammon. Computer Simulation of Protein-Protein Association Kinetics: Acetylcholinesterase-Fasciculin. J. Mol. Biol. 291, 149-162 (1999). [PubMed]
  103. Carlson, H.A., K.M. Masukawa, J.A. McCammon. Method for Including the Dynamic Fluctuations of a Protein in Computer-Aided Drug Design. J. Phys. Chem. A 103, 10213-10219 (1999).
  104. Sept, D., J. Xu, T.D. Pollard, J.A. McCammon. Annealing Accounts for the Length of Actin Filaments Formed by Spontaneous Polymerization. Biophys. J. 77, 2911-2919 (1999). [PubMed]
  105. Masukawa, K.M., H.A. Carlson, J.A. McCammon. Technique for Developing a Pharmacophore Model that Accommodates Inherent Protein Flexibility: An Application to HIV-1 Integrase. In "Pharmacophore Perception, Development, and Use in Drug Design," O.F. Güner, Ed., International University Line, La Jolla, CA, pp. 409-427 (1999).
  106. Sept, D., A.H. Elcock, J.A. McCammon. Computer Simulations of Actin Polymerization Can Explain the Barbed-Pointed End Asymmetry. J. Mol. Biol. 294, 1181-1189 (1999). [PubMed]

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