Publications 1990 - 1994

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  1. Sines, J., S.A. Allison, A. Wierzbicki, J.A. McCammon. Brownian Dynamics Simulation of the Superoxide-Superoxide Dismutase Reaction: Iron and Manganese Enzymes. J. Phys. Chem. 94, 959-961 (1990).
  2. McCammon, J.A. Dynamic Simulation and its Applications in Drug Research. In "Comprehensive Medicinal Chemistry," Vol. 4, C. Hansch, Ed., Pergamon Press, New York, pp. 139-152 (1990).
  3. Subramaniam, S., J.A. McCammon. Molecular Simulations of Biological Systems. In "Theoretical Chemistry and Magnetic Resonance," K.D. Sen, Ed. (1990).
  4. Straatsma, T.P., J.A. McCammon. Molecular Dynamics Simulations with Interaction Potentials Including Polarization. Development of a Noniterative Method and Application to Water. Mol. Sim. 5, 181-192 (1990).
  5. Shen, J., C.F. Wong, S. Subramaniam, T.A. Albright, J.A. McCammon. Partial Electrostatic Charges for the Active Center of Cu, Zn Superoxide Dismutase. J. Comput. Chem. 11, 346-350 (1990).
  6. Mazor, M.H., C.F. Wong, J.A. McCammon, J.M. Deutch, G. Whitesides. Effective Molarity in Diffusion-Controlled Reactions. J. Phys. Chem. 94, 3807-3812 (1990).
  7. Davis, M.E., J.A. McCammon. Calculating Electrostatic Forces from Grid-Calculated Potentials. J. Comput. Chem. 11, 401-409 (1990).
  8. Zheng, C., C.F. Wong, J.A. McCammon. Fluctuation of the Solvent-Accessible Surface Area of Tuna Ferrocytochrome c. Biopolymers 29, 1877-1883 (1990). [PubMed]
  9. Mazor, M.H., J.A. McCammon, T.P. Lybrand. Molecular Recognition in Nonaqueous Solvents. II. Structural and Thermodynamic Analysis of Cationic Selectivity of 18-crown-6 in Methanol. J. Amer. Chem. Soc. 112, 4411-4419 (1990).
  10. Clark, T.W., J.A. McCammon. Parallelization of a Molecular Dynamics Non-Bonded Force Algorithm for MIMD Architecture. Comput. & Chem. 14, 219-224 (1990).
  11. Davis, M.E., J.A. McCammon. Electrostatics in Biomolecular Structure and Dynamics. Chem. Revs. 90, 509-521 (1990).
  12. Sines, J.J., S.A. Allison, J.A. McCammon. Point Charge Distributions and Electrostatic Steering in Enzyme/Substrate Encounter: Brownian Dynamics of Modified Copper/Zinc Superoxide Dismutases. Biochemistry 29, 9403-9412 (1990). [PubMed]
  13. Zheng, C., C.F. Wong, J.A. McCammon. Fluctuation of the Solvent-Accessible Surface Area of Tuna Ferrocytochrome c. In "Science at the John von Neumann National Supercomputer Center," G. Cook, Ed., John von Neumann Center, Princeton University, pp. 221-226 (1990).
  14. Straatsma, T.P., J.A. McCammon. ARGOS, a Vectorized General Molecular Dynamics Program. J. Comput. Chem. 11, 943-951 (1990).
  15. Straatsma, T.P., J.A. McCammon. Free Energy Thermodynamic Integrations in Molecular Dynamics Simulations Using a Noniterative Method to Include Electronic Polarization. Chem. Phys. Letters 167, 252-254 (1990).
  16. Pomès, R., J.A. McCammon. Mass and Step Length Optimization for the Calculation of Equilibrium Properties by Molecular Dynamics Simulation. Chem. Phys. Letters 166, 425-428 (1990).
  17. Shen, J., C.F. Wong, J.A. McCammon. Hydration of Superoxide Studied by Molecular Dynamics Simulation. J. Comput. Chem. 11, 1003-1008 (1990).
  18. Allison, S.A., J.A. McCammon, J.J. Sines. Brownian Dynamics Simulations of Diffusion-Influenced Reactions: Inclusion of Intrinsic Reactivity and Gating. J. Phys. Chem. 94, 7133-7136 (1990).
  19. Zheng, C., M.E. Davis, J.A. McCammon. Electric-Field Distribution inside the Bacterial Photosynthetic Reaction Center of Rhodopseudomonas viridis. Chem. Phys. Letters 173, 246-252 (1990).
  20. Jaroszewski, L., B. Lesyng, J.J. Tanner, J.A. McCammon. Ab Initio Study of Proton Transfer in [H3N-H-NH3]+ and [H3N-H-OH2]+. Chem. Phys. Letters 175, 282-288 (1990).
  21. Wheeler, R.A., J.A. McCammon. π Orbitals in Quantum Path Integral Simulations of Electron Transfer Paths. Chem. Phys. Letters 174, 369-376 (1990).
  22. Wade, R.C., M.H. Mazor, J.A. McCammon, F.A. Quiocho. Hydration of Cavities in Proteins: A Molecular Dynamics Approach. J. Amer. Chem. Soc. 112, 7057-7059 (1990).
  23. Chiu, S.-W., L.K. Nicholson, M.T. Brenneman, S. Subramaniam, Q. Teng, J.A. McCammon, T.A. Cross, E. Jakobsson. Molecular Dynamics Computations and Solid State Nuclear Magnetic Resonance of the Gramicidin Cation Channel. Biophys. J. 60, 974-978 (1991). [PubMed]
  24. McCammon, J.A. Molecular Recognition, Encounter and Complex Formation in Solution. In "Theoretical Biochemistry and Molecular Biophysics, Vol. 2: Proteins," D.L. Beveridge and R. Lavery, Eds., Adenine Press, pp. 121-130 (1991).
  25. Mitchell, M.J., J.A. McCammon. Vector Optimization of AMBER 3.0 on the NEC SX2-400 Supercomputer. Comput. & Chem. 15, 79-85 (1991).
  26. Davis, M.E., J.D. Madura, B.A. Luty, J.A. McCammon. Electrostatics and Diffusion of Molecules in Solution: Simulations with the University of Houston Brownian Dynamics Program. Comput. Phys. Commun. 62, 187-197 (1991).
  27. Chiu, S.-W., E. Jakobsson, S. Subramaniam, J.A. McCammon. Time-Correlation Analysis of Simulated Water Motion in Flexible and Rigid Gramicidin Channels. Biophys. J. 60, 273-285 (1991). [PubMed]
  28. Mitchell, M.J., J.A. McCammon. Free Energy Difference Calculations by Thermodynamic Integration: Difficulties in Obtaining a Precise Value. J. Comput. Chem. 12, 271-275 (1991).
  29. Wade, R.C., M.H. Mazor, J.A. McCammon, F.A. Quiocho. A Molecular Dynamics Study of Thermodynamic and Structural Aspects of the Hydration of Cavities in Proteins. Biopolymers 31, 919-931 (1991). [PubMed]
  30. Straatsma, T.P., J.A. McCammon. Theoretical Calculations of Relative Affinities of Binding. Methods in Enzymol. 202, 497-511 (1991). [PubMed]
  31. Davis, M.E., J.D. Madura, J. Sines, B.A. Luty, S.A. Allison, J.A. McCammon. Diffusion-Controlled Enzymatic Reactions. Methods in Enzymol. 202, 473-497 (1991). [PubMed]
  32. Straatsma, T.P., J.A. McCammon. Multiconfiguration Thermodynamic Integration. J. Chem. Phys. 95, 1175-1188 (1991).
  33. Straatsma, T.P., J.A. McCammon. Free Energy Evaluation from Molecular Dynamics Simulations Using Force Fields Including Electronic Polarization. Chem. Phys. Letters 177, 433-440 (1991).
  34. McCammon, J.A. Free Energy from Simulations. Curr. Opin. Struct. Biol. 1, 196-200 (1991).
  35. Davis, M.E., J.A. McCammon. Dielectric Boundary Smoothing in Finite Difference Solutions of the Poisson Equation: An Approach to Improve Accuracy and Convergence. J. Comput. Chem. 12, 909-912 (1991).
  36. Zheng, C., J.A. McCammon, P.G. Wolynes. Quantum Simulations of Conformation Reorganization in the Electron Transfer Reactions of Tuna Cytochrome c. Chem. Phys. 158, 261-270 (1991).
  37. Shen, J., J.A. McCammon. Molecular Dynamics Simulation of Superoxide Interacting with Superoxide Dismutase. Chem. Phys. 158, 191-198 (1991).
  38. Truong, T.N., J.A. McCammon. Direct Dynamics Study of Intramolecular Proton Transfer in Hydrogenoxalate Anion. J. Amer. Chem. Soc. 113, 7504-7508 (1991).
  39. Tanner, J.J., L.J. Nell, J.A. McCammon. Anti-Insulin Antibody Structure and Conformation. II. Molecular Dynamics With Explicit Solvent. Biopolymers 32, 23-31 (1992). [PubMed]
  40. Nell, L.J., J.A. McCammon, S. Subramaniam. Anti-Insulin Antibody Structure and Conformation. I. Molecular Modeling and Mechanics of an Insulin Antibody. Biopolymers 32, 11-21 (1992). [PubMed]
  41. Sines, J.J., J.A. McCammon, S.A. Allison. Kinetic Effects of Multiple Charge Modifications in Enzyme-Substrate Reactions: Brownian Dynamics Simulations of Cu, Zn Superoxide Dismutase. J. Comput. Chem. 13, 66-69 (1992).
  42. Clark, T.W., J.A. McCammon, L.R. Scott. Parallel Molecular Dynamics. In "Proc. Fifth SIAM Conf. on Parallel Proc. for Sci. Comp.," J. Dongarra, et al., Eds., SIAM, Philadelphia, pp. 338-344 (1992, refereed).
  43. Truong, T.N., J.J. Tanner, P. Bała, J.A. McCammon, D.J. Kouri, B. Lesyng, D.K. Hoffman. A Comparative Study of Time Dependent Quantum Mechanical Wavepacket Evolution Methods. J. Chem. Phys. 96, 2077-2084 (1992).
  44. Wade, R.C., J.A. McCammon. Binding of an Antiviral Agent to a Sensitive and a Resistant Human Rhinovirus. Computer Simulation Studies with Sampling of Amino Acid Side-chain Conformations. I. Mapping the Rotamers of Residue 188 of Viral Protein 1. J. Mol. Biol. 225, 679-696 (1992). [PubMed]
  45. Wade, R.C., J.A. McCammon. Binding of an Antiviral Agent to a Sensitive and a Resistant Human Rhinovirus. Computer Simulation Studies with Sampling of Amino Acid Side-chain Conformations. II. Calculation of Free Energy Differences by Thermodynamic Integration. J. Mol. Biol. 225, 697-712 (1992). [PubMed]
  46. Straatsma, T.P., J.A. McCammon. Computational Alchemy. Ann. Rev. Phys. Chem. 43, 407-435 (1992).
  47. Bała, P., B. Lesyng, T.N. Truong, J.A. McCammon. Ab Initio Studies and Quantum-Classical Molecular Dynamics Simulations for Proton Transfer Processes in Model Systems and in Enzymes. In "Molecular Aspects of Biotechnology: Computational Models and Theories," J. Bertran, Ed., NATO, pp. 299-326 (1992).
  48. Truong, T.N., J.A. McCammon, D.J. Kouri, D.K. Hoffman. A Combined Quantum-Classical Dynamics Method for Calculating Thermal Rate Constants of Chemical Reactions in Solution. J. Chem. Phys. 96, 8136-8142 (1992).
  49. Luty, B., M.E. Davis, J.A. McCammon. Electrostatic Energy Calculations by a Finite-Difference Method: Rapid Calculation of Charge-Solvent Interaction Energies. J. Comput. Chem. 13, 768-771 (1992).
  50. Mohan, V., M.E. Davis, J.A. McCammon, B.M. Pettitt. Continuum Model Calculations of Solvation Free Energies: Accurate Evaluation of Electrostatic Contributions. J. Phys. Chem. 96, 6428-6431 (1992).
  51. Briggs, J.M., J.A. McCammon. Computation Unravels Mysteries of Molecular Biophysics. Comput. in Phys. 6, 238-243 (1992).
  52. Luty, B.A., M.E. Davis, J.A. McCammon. Solving the Finite-Difference Non-Linear Poisson-Boltzmann Equation. J. Comput. Chem. 13, 1114-1118 (1992).
  53. Zacharias, M., B.A. Luty, M.E. Davis, J.A. McCammon. Poisson-Boltzmann Analysis of the Lambda Repressor-Operator Interaction. Biophys. J. 63, 1280-1285 (1992). [PubMed]
  54. Straatsma, T.P., M. Zacharias, J.A. McCammon. Holonomic Constraint Contributions to Energy Differences from Thermodynamic Integration Molecular Dynamics Simulations. Chem. Phys. Letters 196, 297-302 (1992).
  55. McCammon, J.A. Superperfect Enzymes. Curr. Biol. 2, 585-586 (1992). [PubMed]
  56. Luty, B.A., J.A. McCammon, H.-X. Zhou. Diffusive Reaction Rates from Brownian Dynamics Simulations: Replacing the Outer Cutoff Surface by an Analytical Treatment. J. Chem. Phys. 97, 5682-5686 (1992).
  57. Wade, R.C., M.E. Davis, B.A. Luty, J.D. Madura, J.A. McCammon. Gating of the Active Site of Triose Phosphate Isomerase: Brownian Dynamics Simulations of Flexible Peptide Loops in the Enzyme. Biophys. J. 64, 9-15 (1993). [PubMed]
  58. Wong, C.F., C. Zheng, J. Shen, J.A. McCammon, P.G. Wolynes. Cytochrome c: A Molecular Proving Ground for Computer Simulations. J. Phys. Chem. 97, 3100-3110 (1993).
  59. Cannon, W.R., J.D. Madura, R.P. Thummel, J.A. McCammon. Molecular Recognition: Effect of Rotational Isomers on Host-Guest Binding. J. Amer. Chem. Soc. 115, 879-884 (1993).
  60. Luty, B.A., R.C. Wade, J.D. Madura, M.E. Davis, J.M. Briggs, J.A. McCammon. Brownian Dynamics Simulations of Diffusional Encounters between Triose Phosphate Isomerase and Glyceraldehyde Phosphate: Electrostatic Steering of Glyceraldehyde Phosphate. J. Phys. Chem. 97, 233-237 (1993).
  61. Wong, Y.-T., T.W. Clark, J. Shen, J.A. McCammon. Molecular Dynamics Simulation of Substrate-Enzyme Interactions in the Active Site Channel of Superoxide Dismutase. Mol. Sim. 10, 277-289 (1993).
  62. Jaroszewski, L., B. Lesyng, J.A. McCammon. Ab Initio Potential Energy Functions for Proton Transfer in [H3N-H-NH3]+ and [H3N-H-OH2]+. J. Mol. Struct. 283, 57-62 (1993).
  63. Tan, R.C., T.N. Truong, J.A. McCammon, J.L. Sussman. Acetylcholinesterase: Electrostatic Steering Increases the Rate of Ligand Binding. Biochemistry 32, 401-403 (1993). [PubMed]
  64. Gilson, M.K., M.E. Davis, B.A. Luty, J.A. McCammon. Computation of Electrostatic Forces on Solvated Molecules Using the Poisson-Boltzmann Equation. J. Phys. Chem. 97, 3591-3600 (1993).
  65. Luty, B.A., J.A. McCammon. Simulation of Bimolecular Reactions: Synthesis of the Encounter and Reaction Steps. Mol. Sim. 10, 61-65 (1993).
  66. Straatsma, T.P., M. Zacharias, J.A. McCammon. Free Energy Difference Calculations in Biomolecular Systems. In "Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications," Vol. 2, W.F. van Gunsteren, P.K. Weiner, and A.J. Wilkinson, Eds., ESCOM Science Publishers B.V., Leiden, pp. 349-367 (1993).
  67. Zacharias, M., T.P. Straatsma, J.A. McCammon, F.A. Quiocho. Inversion of Receptor Binding Preferences by Mutagenesis: Free Energy Thermodynamic Integration Studies on Sugar-Binding to L-Arabinose Binding Proteins. Biochemistry 32, 7428-7434 (1993). [PubMed]
  68. Luty, B.A., S. El Amrani, J.A. McCammon. Simulation of the Bimolecular Reaction between Superoxide and Superoxide Dismutase: Synthesis of the Encounter and Reaction Steps. J. Amer. Chem. Soc. 115, 11874-11877 (1993).
  69. Potter, M.J., M.K. Gilson, J.A. McCammon. Small Molecule pKa Prediction with Continuum Electrostatics Calculations. J. Amer. Chem. Soc. 116, 10298-10299 (1994).
  70. Madura, J.D., M.E. Davis, M.K. Gilson, R.C. Wade, B.A. Luty, J.A. McCammon. Biological Applications of Electrostatic Calculations and Brownian Dynamics Simulations. Revs. Comput. Chem. 5, 229-267 (1994).
  71. Bała, P., B. Lesyng, J.A. McCammon. Extended Hellmann-Feynman Theorem for Non-Stationary States and Its Application in Quantum-Classical Molecular Dynamics Simulations. Chem. Phys. Letters 219, 259-266 (1994).
  72. Wade, R.C., B.A. Luty, E. Demchuk, J.D. Madura, M.E. Davis, J.M. Briggs, J.A. McCammon. Simulation of Enzyme-Substrate Encounter with Gated Active Sites. Nature Struct. Biol. 1, 65-69 (1994). [PubMed]
  73. Bała, P., B. Lesyng, J.A. McCammon. Applications of Quantum-Classical and Quantum-Stochastic Molecular Dynamics Simulations for Proton Transfer Processes. Chem. Phys. 180, 271-285 (1994).
  74. McCammon, J.A., B.M. Pettitt, L.R. Scott. Ordinary Differential Equations of Molecular Dynamics. Comput. Math. Applic. 28, 319-326 (1994).
  75. Zacharias, M., T.P. Straatsma, J.A. McCammon. Separation-shifted Scaling, a new Scaling Method for Lennard-Jones Interactions in Thermodynamic Integration. J. Chem. Phys. 100, 9025-9031 (1994).
  76. Lesyng, B., J.A. McCammon. Molecular Modeling Methods. Basic Techniques and Challenging Problems. Pharmacol. Therapeut. 60, 149-167 (1994). [PubMed]
  77. Gilson, M.K., T.P. Straatsma, J.A. McCammon, D.R. Ripoll, C.H. Faerman, P.H. Axelsen, I. Silman, J.L. Sussman. Open "Back Door" in a Molecular Dynamics Simulation of Acetylcholinesterase. Science 263, 1276-1278 (1994). [PubMed]
  78. Antosiewicz, J., J.A. McCammon, M.K. Gilson. Prediction of pH-Dependent Properties of Proteins. J. Mol. Biol. 238, 415-436 (1994). [PubMed]
  79. Zacharias, M., B.A. Luty, M.E. Davis, J.A. McCammon. Combined Conformational Search and Finite-Difference Poisson-Boltzmann Approach for Flexible Docking. Application to an Operator Mutation in the Lambda Repressor-Operator Complex. J. Mol. Biol. 238, 455-465 (1994). [PubMed]
  80. Antosiewicz, J., M.K. Gilson, J.A. McCammon. Acetylcholinesterase: Effects of Ionic Strength and Dimerization on the Rate Constants. Israel J. Chem. 34, 151-158 (1994).
  81. McCammon, J.A. Free Energy and Binding Selectivity. In "Computational Approaches in Supramolecular Chemistry," G. Wipff, Ed., Kluwer Acad. Pub., Dordrecht, pp. 515-517 (1994).
  82. Cannon, W.R., B.M. Pettitt, J.A. McCammon. Sulfate Anion in Water: Model Structural, Thermodynamic, and Dynamic Properties. J. Phys. Chem. 98, 6225-6230 (1994).
  83. Clark, T.W., R. von Hanxleden, J.A. McCammon, L.R. Scott. Parallelization using Spatial Decomposition for Molecular Dynamics. In "Scalable High Performance Computing Conference," IEEE Computer Society, pp. 95-102 (1994, refereed).
  84. Marrone, T.J., J.A. McCammon. Pepzyme Dynamics and Conformation: A Molecular Dynamics Study in Water. J. Amer. Chem. Soc. 116, 6987-6988 (1994).
  85. Straatsma, T.P., J.A. McCammon. Treatment of Rotational Isomeric States III. The Use of Biasing Potentials. J. Chem. Phys. 101, 5032-5039 (1994).

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