Publications 1985 - 1989


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  1. Allison, S.A., J.A. McCammon. Dynamics of Substrate Binding to Copper Zinc Superoxide Dismutase. J. Phys. Chem. 89, 1072-1074 (1985).
  2. Prabhakaran, M., J.A. McCammon, S.C. Harvey. Atomic Motions in Phenylalanine Transfer RNA Probed by Molecular Dynamics Simulations. In "The Molecular Basis of Cancer, Part A: Macromolecular Structure, Carcinogens, and Oncogenes," R. Rein, Ed., Alan R. Liss, New York, pp. 123-129 (1985). [PubMed]
  3. Harvey, S.C., M. Prabhakaran, J.A. McCammon. Molecular-Dynamics Simulation of Phenylalanine Transfer RNA. I. Methods and General Results. Biopolymers 24, 1169-1188 (1985). [PubMed]
  4. Prabhakaran, M., S.C. Harvey, J.A. McCammon. Molecular-Dynamics Simulation of Phenylalanine Transfer RNA. II. Amplitudes, Anisotropies and Anharmonicities of Atomic Motions. Biopolymers 24, 1189-1204 (1985). [PubMed]
  5. Dickinson, E., S.A. Allison, J.A. McCammon. Brownian Dynamics with Rotation-Translation Coupling. J. Chem. Soc., Faraday Trans. II 81, 591-601 (1985).
  6. Allison, S.A., G. Ganti, J.A. McCammon. Simulation of the Diffusion-Controlled Reaction Between Superoxide and Superoxide Dismutase. I. Simple Models. Biopolymers 24, 1323-1336 (1985). [PubMed]
  7. McCammon, J.A. Molecular Dynamics with Stochastic Boundary Conditions. In "Molecular Dynamics and Protein Structure," J. Hermans, Ed., University of North Carolina, Chapel Hill, p. 15 (1985).
  8. McCammon, J.A. Simulation of Activated Processes. In "Molecular Dynamics and Protein Structure," J. Hermans, Ed., University of North Carolina, Chapel Hill, pp. 103-104 (1985).
  9. McCammon, J.A. Simulation of Diffusional Encounters. In "Molecular Dynamics and Protein Structure," J. Hermans, Ed., University of North Carolina, Chapel Hill, pp. 65-66 (1985).
  10. McCammon, J.A., S.A. Allison, S.H. Northrup. Theoretical Molecular Biology: Some Recent Developments. J. Mol. Sci. (China) 3, 193-204 (1985, Invited review).
  11. Ganti, G., J.A. McCammon, S.A. Allison. Brownian Dynamics of Diffusion-Controlled Reactions: The Lattice Method. J. Phys. Chem. 89, 3899-3902 (1985).
  12. Karplus, M., J.A. McCammon. Dynamics of Proteins: Elements and Function. In "Protein and Nucleic Acid Structure and Dynamics," J. King, Ed., Benjamin Cummings, Inc., pp. 169-206 (1985).
  13. Allison, S.A., S.H. Northrup, J.A. McCammon. Extended Brownian Dynamics of Diffusion Controlled Reactions. J. Chem. Phys. 83, 2894-2899 (1985).
  14. Harvey, S.C., M. Prabhakaran, F.L. Suddath, J.A. McCammon. Computer Graphics and Moving Pictures in the Analysis of Intramolecular Motions in Phenylalanine Transfer RNA. In "Molecular Dynamics and Protein Structure," J. Hermans, Ed., University of North Carolina, Chapel Hill, p. 161 (1985).
  15. Lybrand, T.P., I. Ghosh, J.A. McCammon. Hydration of Chloride and Bromide Anions: Determination of Relative Free Energy by Computer Simulation. J. Amer. Chem. Soc. 107, 7793-7794 (1985).
  16. McCammon, J.A., S.H. Northrup, S.A. Allison. Diffusional Dynamics of Ligand-Receptor Association. J. Phys. Chem. 90, 3901-3905 (1986, Invited Feature Article).
  17. Allison, S.A., J.A. McCammon, S.H. Northrup. Dynamics of Macromolecular Interactions. In "Coulombic Interactions in Macromolecular Systems," A. Eisenberg and F.E. Bailey, Eds., American Chemical Society, Washington, D.C., pp. 216-231 (1986).
  18. Allison, S.A., S.H. Northrup, J.A. McCammon. Simulation of Biomolecular Diffusion and Complex Formation. In "Macromolecular Assembly Analyzed by Converging Structural Techniques," V.A. Parsegian, Ed., Rockefeller University Press, New York, N.Y., pp. 167-175 (1986).
  19. McCammon, J.A., T.P. Lybrand, S.A. Allison, S.H. Northrup. Ligand Binding: New Theoretical Approaches to Molecular Recognition. In "Biomolecular Stereodynamics III," R.H. Sarma, Ed., Adenine Press, N.Y., pp. 227-235 (1986).
  20. Lybrand, T.P., J.A. McCammon, G. Wipff. Theoretical Calculation of Relative Binding Affinity in Host-Guest Systems. Proc. Natl. Acad. Sci. USA 83, 833-835 (1986). [PubMed]
  21. Belch, A.C., M. Berkowitz, J.A. McCammon. Solvation Structure of a Sodium Chloride Ion Pair in Water. J. Amer. Chem. Soc. 108, 1755-1761 (1986).
  22. Bruccoleri, R.E., M. Karplus, J.A. McCammon. The Hinge-Bending Mode of a Lysozyme-Inhibitor Complex. Biopolymers 25, 1767-1802 (1986). [PubMed]
  23. Karplus, M., J.A. McCammon. Dynamics of Proteins. Scientific American 254, 42-51 (1986, April, Invited review). [PubMed]
  24. Ganti, G., J.A. McCammon. Transport Properties of Macromolecules by Brownian Dynamics Simulation: Vectorization of Brownian Dynamics on the Cyber-205. J. Comput. Chem. 7, 457-463 (1986).
  25. McCammon, J.A., O.A. Karim, T.P. Lybrand, C.F. Wong. Ionic Association in Water: From Atoms to Enzymes. Ann. N.Y. Acad. Sci. 482, 210-221 (1986). [PubMed]
  26. Karim, O.A., J.A. McCammon. Dynamics of a Sodium Chloride Ion Pair in Water. J. Amer. Chem. Soc. 108, 1762-1766 (1986).
  27. Northrup, S.H., M.S. Curvin, S.A. Allison, J.A. McCammon. Optimization of Brownian Dynamics Methods for Diffusion-Influenced Rate Constant Calculations. J. Chem. Phys. 84, 2196-2203 (1986).
  28. Bacquet, R.J., J.A. McCammon. Salt Effects on Enzyme-Substrate Interactions by Monte Carlo Simulation. Ann. N.Y. Acad. Sci. 482, 245-247 (1986). [PubMed]
  29. Lopez, J.P., T.A. Albright, J.A. McCammon. The Interaction of O2- with Water. Chem. Phys. Letters 125, 454-458 (1986).
  30. Case, D.A., J.A. McCammon. Dynamic Simulations of Oxygen Binding to Myoglobin. Ann. N.Y. Acad. Sci. 482, 222-233 (1986). [PubMed]
  31. Wong, C.F., J.A. McCammon. Dynamics and Design of Enzymes and Inhibitors. J. Amer. Chem. Soc. 108, 3830-3832 (1986).
  32. Wong, C.F., J.A. McCammon. Computer Simulation and the Design of New Biological Molecules. Israel J. Chem. 27, 211-215 (1986, Invited article).
  33. Allison, S.A., S.H. Northrup, J.A. McCammon. Simulation of Biomolecular Diffusion and Complex Formation. Biophys. J. 49, 167-175 (1986). [PubMed]
  34. Ganti, G., J.A. McCammon. Substrate Steering by Electrostatic Fields of Enzymes: Visualization by Computer Graphics. J. Mol. Graphics 4, 200-202 (1986).
  35. Richards, F., R. Baldwin, G.R. Galluppi, R. Griffin, E.T. Kaiser, B. Matthews, J.A. McCammon, A. Redfield, B. Reid, R. Sauer, A. Schechter, P. Sigler, P. von Hippel, D. Wiley. Report of the Research Briefing Panel on Protein Structure and Biological Function. In "Research Briefings 1986," National Academy Press, Washington, D.C., pp. 37-48 (1986).
  36. Karim, O.A., J.A. McCammon. Rate Constants for Ion Pair Formation and Dissociation in Water. Chem. Phys. Letters 132, 219-224 (1986).
  37. Wong, C.F., J.A. McCammon. Thermodynamics of Enzyme Folding and Activity: Theory and Experiment. In "Structure, Dynamics and Function of Biomolecules," A. Ehrenberg and R. Rigler, Eds., Springer-Verlag, Berlin, pp. 51-55 (1987).
  38. McCammon, J.A. Molecular Recognition. Physics Today 40, S12-S13 (1987).
  39. Ghosh, I., J.A. McCammon. Sidechain Rotational Isomerization in Proteins: Dynamic Simulation with Solvent Surroundings. Biophys. J. 51, 637-641 (1987). [PubMed]
  40. Ghosh, I., J.A. McCammon. Solvent Viscosity Effects on the Rate of Side-Chain Rotational Isomerization in a Protein Molecule. J. Phys. Chem. 91, 4878-4881 (1987).
  41. McCammon, J.A., R.J. Bacquet, S.A. Allison, S.H. Northrup. Trajectory Simulation Studies of Diffusion-Controlled Reactions. Faraday Discuss. Chem. Soc. 83, 213-222 (1987). [PubMed]
  42. Lybrand, T.P., W.F. Lau, J.A. McCammon, B.M. Pettitt. Molecular Dynamics Studies on Antiviral Agents: Thermodynamics of Solvation and Binding. In "Protein Structure and Design," UCLA Symposia on Molecular and Cellular Biology, New Series, Vol. 69, D. Oxender, Ed., Alan R. Liss, Inc., New York, pp. 227-233 (1987).
  43. Hubbard, J.B., J.A. McCammon. Electrophoretic Light Scattering from Macromolecular Solutions and Conformational Dynamics. J. Chem. Phys. 87, 4339-4343 (1987).
  44. McCammon, J.A. Computer-Aided Molecular Design. Science 238, 486-491 (1987, Invited article). [PubMed]
  45. Madura, J.D., B.M. Pettitt, J.A. McCammon. Geometric Considerations in the Calculation of Relative Free Energies of Activation. Chem. Phys. Letters 141, 83-87 (1987).
  46. Allison, S.A., R.J. Bacquet, J.A. McCammon. Simulation of the Diffusion-Controlled Reaction Between Superoxide and Superoxide Dismutase. II. Detailed Models. Biopolymers 27, 251-269 (1988). [PubMed]
  47. Wilcox, G.L., F.A. Quiocho, C. Levinthal, S.C. Harvey, G.M. Maggiora, J.A. McCammon. Symposium Overview. Minnesota Conference on Supercomputing in Biology: Proteins, Nucleic Acids, and Water. J. Comput.-Aided Mol. Des. 1, 271-281 (1988). [PubMed]
  48. Zheng, C., C.F. Wong, J.A. McCammon, P.G. Wolynes. Quantum Simulation of Ferrocytochrome c. Nature 334, 726-728 (1988). [PubMed]
  49. Bacquet, R.J., J.A. McCammon, S.A. Allison. Ionic Strength Dependence of Enzyme-Substrate Interactions. Monte Carlo and Poisson-Boltzmann Results for Superoxide Dismutase. J. Phys. Chem. 92, 7134-7141 (1988).
  50. Wong, C.F., J.A. McCammon. Computer Simulation of Proteins: Classical and Quantum Dynamics. In "Science at the John von Neumann Center, 1987," L. Anacker, Ed., John von Neumann Center, Princeton University, pp. 131-134 (1988).
  51. McCammon, J.A., G. Ganti, T.P. Lybrand, C.F. Wong. Supercomputer Simulation and Biomolecular Design. In "High Speed Computing, Scientific Applications and Algorithm Design," R.B. Wilhelmson, Ed., University of Illinois Press, pp. 155-161 (1988).
  52. Wong, C.F., J.A. McCammon. Molecular Dynamics Simulation Studies of Water and Protein Solutions. In "Science on the ETA10," L. Anacker, Ed., John Von Neumann Center, Princeton University, pp. 72-77 (1988).
  53. Lybrand, T.P., J.A. McCammon. Computer Simulation Study of the Binding of an Antiviral Agent to a Sensitive and a Resistant Human Rhinovirus. J. Comput.-Aided Mol. Des. 2, 259-266 (1989). [PubMed]
  54. Sridharan, S., J.A. McCammon, J.B. Hubbard. Diffusion-Controlled Reactions of Ions in Fluctuating Ionic Atmospheres. J. Chem. Phys. 90, 237-240 (1989).
  55. Mazor, M.H., J.A. McCammon, T.P. Lybrand. Molecular Recognition in Nonaqueous Solvents: Na+, K+, and 18-crown-6 in Methanol. J. Amer. Chem. Soc. 111, 55-56 (1989).
  56. Madura, J.D., B.M. Pettitt, J.A. McCammon. Methods for Calculating Geometries of Transition States in Solution. Chem. Phys. 129, 185-191 (1989).
  57. Sauniere, J.C., T.P. Lybrand, J.A. McCammon, L.D. Pyle. Polarizable Water Models: Vectorization of Energy Calculations on the CYBER 205. Comput. & Chem. 13, 313-317 (1989).
  58. Davis, M.E., J.A. McCammon. Solving the Finite Difference Linearized Poisson-Boltzmann Equation: A Comparison of Relaxation and Conjugate Gradient Methods. J. Comput. Chem. 10, 386-391 (1989).
  59. Straatsma, T.P., J.A. McCammon. Treatment of Rotational Isomers in Free Energy Evaluations. Analysis of the Evaluation of Free Energy Differences by Molecular Dynamics Simulations of Systems with Rotational Isomeric States. J. Chem. Phys. 90, 3300-3304 (1989).
  60. Wong, C.F., C. Zheng, J.A. McCammon. Glass Transition in SPC/E Water and in a Protein Solution: A Molecular Dynamics Simulation Study. Chem. Phys. Letters 154, 151-154 (1989).
  61. Subramaniam, S., J.A. McCammon. Molecular Recognition. In "McGraw-Hill Yearbook of Science and Technology, 1990. (Supplement to Encyclopedia of Science and Technology, 6th Ed.)," pp. 213-215 (1989).
  62. Jordan, P.C., R.J. Bacquet, J.A. McCammon, P. Tran. How Electrolyte Shielding Influences the Electrical Potential in Transmembrane Ion Channels. Biophys. J. 55, 1041-1052 (1989). [PubMed]
  63. Subramaniam, S., J.A. McCammon, R.J. Bacquet. Probing Molecular Recognition Using Simulation Methods. In "The Immune Response to Structurally Defined Proteins: The Lysozyme Model," S.J. Smith-Gill and E. Sercarz, Eds., Adenine Press, pp. 169-176 (1989).
  64. McCammon, J.A., C.F. Wong, T.P. Lybrand. Protein Stability and Function: Theoretical Studies. In "Prediction of Protein Structure and the Principles of Protein Conformation," G.D. Fasman, Ed., Plenum, New York, pp. 149-159 (1989).
  65. Shen, J., S. Subramaniam, C.F. Wong, J.A. McCammon. Superoxide Dismutase: Fluctuations in the Structure and Solvation of the Active Site Channel Studied by Molecular Dynamics Simulation. Biopolymers 28, 2085-2096 (1989). [PubMed]
  66. Chiu, S.-W., S. Subramaniam, E. Jakobsson, J.A. McCammon. Water and Polypeptide Conformations in Gramicidin Channel - A Molecular Dynamics Study. Biophys. J. 56, 253-261 (1989). [PubMed]
  67. Wong, C.F., J. Shen, C. Zheng, S. Subramaniam, J.A. McCammon. Molecular Dynamics Simulation of Protein Hydration: Studies on Tuna Ferrocytochrome-c and Bovine Erythrocyte Superoxide Dismutase. J. Mol. Liq. 41, 193-206 (1989, Special issue in honor of G. Careri).
  68. Zheng, C., C.F. Wong, J.A. McCammon, P.G. Wolynes. Classical and Quantum Aspects of Ferrocytochrome-c. Chemica Scripta 29A, 171-179 (1989, Proceedings of Nobel Symposium).
  69. Straatsma, T.P., J.A. McCammon. Treatment of Rotational Isomers in Free Energy Calculations. II. Molecular Dynamics Simulation Study of 18-crown-6 in Aqueous Solution as an Example of Systems with Large Numbers of Rotational Isomeric States. J. Chem. Phys. 91, 3631-3637 (1989).
  70. Zheng, C., J.A. McCammon, P.G. Wolynes. Quantum Simulation of Nuclear Rearrangement in Electron Transfer Reactions. Proc. Natl. Acad. Sci. USA 86, 6441-6444 (1989). [PubMed]
  71. Madura, J.D., J.A. McCammon. Brownian Dynamics Simulation of Diffusional Encounters Between Triose Phosphate Isomerase and D-Glyceraldehyde Phosphate. J. Phys. Chem. 93, 7285-7287 (1989).

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