Publications 1980 - 1984


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  1. Northrup, S.H., J.A. McCammon. Efficient Trajectory Simulation Methods for Diffusional Barrier Crossing Processes. J. Chem. Phys. 72, 4569-4578 (1980).
  2. Northrup, S.H., J.A. McCammon. Simulation Methods for Protein Structure Fluctuations. Biopolymers 19, 1001-1016 (1980). [PubMed]
  3. Karplus, M., B.R. Gelin, J.A. McCammon. Internal Dynamics of Proteins: Short Time and Long Time Motions of Aromatic Sidechains in PTI. Biophys. J. 32, 603-618 (1980). [PubMed]
  4. Levy, R.M., M. Karplus, J.A. McCammon. Molecular Dynamics Studies of NMR Relaxation in Proteins. Biophys. J. 32, 628-630 (1980). [PubMed]
  5. McCammon, J.A., M. Karplus. Simulation of Protein Dynamics. Ann. Rev. Phys. Chem. 31, 29-45 (1980, Invited review).
  6. McCammon, J.A., M. Karplus. Dynamics of Tyrosine Ring Rotations in a Globular Protein. Biopolymers 19, 1375-1405 (1980).
  7. Northrup, S.H., M.R. Pear, J.A. McCammon, M. Karplus. Molecular Dynamics of Ferrocytochrome c. Nature 286, 304-305 (1980). [PubMed]
  8. Karplus, M., B.R. Gelin, J.A. McCammon. Internal Dynamics of Proteins: Short Time and Long Time Motions of Aromatic Sidechains in PTI. In "Proteins and Nucleoproteins: Structure, Dynamics and Assembly," V.A. Parsegian, Ed., Rockefeller University Press, New York, N.Y., pp. 603-618 (1980).
  9. Levy, R.M., M. Karplus, J.A. McCammon. Molecular Dynamics Studies of NMR Relaxation in Proteins. In "Proteins and Nucleoproteins: Structure, Dynamics and Assembly," V.A. Parsegian, Ed., Rockefeller University Press, New York, N.Y., pp. 628-629 (1980).
  10. McCammon, J.A., S.H. Northrup, M. Karplus, R.M. Levy. Helix-Coil Transitions in a Simple Polypeptide Model. Biopolymers 19, 2033-2045 (1980).
  11. Pear, M.R., S.H. Northrup, J.A. McCammon. Diffusional Correlations in Polymer Dynamics. J. Chem. Phys. 73, 4703-4704 (1980).
  12. Northrup, S.H., M.R. Pear, J.A. McCammon, M. Karplus, T. Takano. Internal Mobility of Ferrocytochrome c. Nature 287, 659-660 (1980). [PubMed]
  13. Karplus, M., J.A. McCammon, W.L. Peticolas. The Internal Dynamics of Globular Proteins. CRC Crit. Rev. Biochem. 9, 293-349 (1981, Invited review). [PubMed]
  14. Northrup, S.H., M.R. Pear, J.D. Morgan, J.A. McCammon. Molecular Dynamics of Ferrocytochrome c: Fluctuation Anisotropy. In "Protein Dynamics and Energy Transduction," S. Ishiwata, Ed., Taniguchi Foundation Press, Japan, pp. 134-162 (1981).
  15. Pear, M.R., S.H. Northrup, J.A. McCammon, M. Karplus, R.M. Levy. Correlated Helix-Coil Transitions in Polypeptides. Biopolymers 20, 629-632 (1981).
  16. Levy, R.M., M. Karplus, J.A. McCammon. Increase of carbon-13 NMR Relaxation Times in Proteins due to Picosecond Motional Averaging. J. Amer. Chem. Soc. 103, 994-996 (1981).
  17. Karplus, M., J.A. McCammon. Pressure Dependence of Aromatic Ring Rotations in Proteins: A Collisional Interpretation. FEBS Letters 131, 34-36 (1981).
  18. Mao, B., M.R. Pear, J.A. McCammon, S.H. Northrup. Repulsive Interactions Between Polar and Apolar Atoms in Globular Proteins. J. Mol. Biol. 151, 199-202 (1981). [PubMed]
  19. Pear, M.R., J.A. McCammon. Hydrodynamic Interaction Effects on Local Motions of Chain Molecules. J. Chem. Phys. 74, 6922-6925 (1981).
  20. Northrup, S.H., M.R. Pear, J.D. Morgan, J.A. McCammon, M. Karplus. Molecular Dynamics of Ferrocytochrome c: Magnitude and Anisotropy of Atomic Displacements. J. Mol. Biol. 153, 1087-1109 (1981). [PubMed]
  21. Berkowitz, M., J.A. McCammon. Brownian Motion of a System of Coupled Harmonic Oscillators. J. Chem. Phys. 75, 957-961 (1981).
  22. Berkowitz, M., J.D. Morgan, D.J. Kouri, J.A. McCammon. Memory Kernels from Molecular Dynamics. J. Chem. Phys. 75, 2462-2463 (1981).
  23. McCammon, J.A., S.H. Northrup. Gated Binding of Ligands to Proteins. Nature 293, 316-317 (1981). [PubMed]
  24. Harvey, S.C., J.A. McCammon. Intramolecular Flexibility in Phenylalanine Transfer RNA. Nature 294, 286-287 (1981). [PubMed]
  25. Northrup, S.H., M.R. Pear, C.-Y. Lee, J.A. McCammon, M. Karplus. Dynamical Theory of Activated Processes in Globular Proteins. Proc. Natl. Acad. Sci. USA 79, 4035-4039 (1982). [PubMed]
  26. Mao, B., M.R. Pear, J.A. McCammon, S.H. Northrup. Molecular Dynamics of Ferrocytochrome c: Anharmonicity of Atomic Displacements. Biopolymers 21, 1979-1989 (1982). [PubMed]
  27. Mao, B., M.R. Pear, J.A. McCammon, F.A. Quiocho. Hinge-bending in L-Arabinose-binding Protein: The "Venus's-Flytrap" Model. J. Biol. Chem. 257, 1131-1133 (1982). [PubMed]
  28. Berkowitz, M., D.J. Kouri, J.A. McCammon. Surface Temperature Effects in Molecule-Surface Collisions. J. Phys. Chem. 86, 2669-2671 (1982).
  29. Northrup, S.H., F. Zarrin, J.A. McCammon. Rate Theory for Gated Diffusion-Influenced Ligand Binding to Proteins. J. Phys. Chem. 86, 2314-2321 (1982).
  30. Berkowitz, M., J.A. McCammon. Molecular Dynamics with Stochastic Boundary Conditions. Chem. Phys. Letters 90, 215-217 (1982).
  31. Harvey, S.C., J.A. McCammon. Macromolecular Conformational Energy Minimization: An Algorithm Varying Pseudodihedral Angles. Comput. & Chem. 6, 173-179 (1982).
  32. Szabo, A., D. Shoup, S.H. Northrup, J.A. McCammon. Stochastically Gated Diffusion-Influenced Reactions. J. Chem. Phys. 77, 4484-4493 (1982).
  33. McCammon, J.A., M. Karplus. The Dynamic Picture of Protein Structure. Acc. Chem. Res. 16, 187-193 (1983, Invited review).
  34. Berkowitz, M., J.D. Morgan, J.A. McCammon. Generalized Langevin Dynamics Simulations with Arbitrary Time-Dependent Memory Kernels. J. Chem. Phys. 78, 3256-3261 (1983).
  35. Morgan, J.D., J.A. McCammon, S.H. Northrup. Molecular Dynamics of Ferrocytochrome c: Time Dependence of the Atomic Displacements. Biopolymers 22, 1579-1593 (1983).
  36. McCammon, J.A., B. Mao. Protein Dynamics. McGraw-Hill Yearbook of Science and Technology, 1984 (Supplement to Encyclopedia of Science and Technology, 5th Ed.), pp. 363-365 (1983, Invited review).
  37. Karplus, M., J.A. McCammon. Dynamics of Proteins: Elements and Function. Ann. Rev. Biochem. 52, 263-300 (1983, Invited review). [PubMed]
  38. McCammon, J.A., C.Y. Lee, S.H. Northrup. Side-Chain Rotational Isomerization in Proteins: A Mechanism Involving Gating and Transient Packing Defects. J. Amer. Chem. Soc. 105, 2232-2237 (1983).
  39. Berkowitz, M., J.D. Morgan, J.A. McCammon, S.H. Northrup. Diffusion-Controlled Reactions: A Variational Formula for the Optimum Reaction Coordinate. J. Chem. Phys. 79, 5563-5565 (1983).
  40. Mao, B., J.A. McCammon. Theoretical Study of Hinge-bending in L-Arabinose-Binding Protein: Internal Energy and Free Energy Changes. J. Biol. Chem. 258, 12543-12547 (1983). [PubMed]
  41. Northrup, S.H., J.A. McCammon. Saddle-Point Avoidance in Diffusional Reactions. J. Chem. Phys. 78, 987-989 (1983).
  42. Prabhakaran, M., S.C. Harvey, B. Mao, J.A. McCammon. Molecular Dynamics of Phenylalanine Transfer RNA. J. Biomol. Struct. Dyn. 1, 357-369 (1983). [PubMed]
  43. Allison, S.A., J.A. McCammon. Transport Properties of Rigid and Flexible Macromolecules by Brownian Dynamics Simulation. Biopolymers 23, 167-187 (1984).
  44. Allison, S.A., J.A. McCammon. Multistep Brownian Dynamics: Application to Short Wormlike Chains. Biopolymers 23, 363-375 (1984). [PubMed]
  45. Levy, R.M., A.R. Srinivasan, W.K. Olson, J.A. McCammon. Quasi-Harmonic Method for Studying Very Low Frequency Modes in Proteins. Biopolymers 23, 1099-1112 (1984). [PubMed]
  46. McCammon, J.A. Computational Biochemistry: From Theoretical Mechanics to the Design of Drugs and Enzymes. For the National Academy of Sciences Report on Frontiers in Chemistry, G.C. Pimentel, Ed. (1984, Invited contribution).
  47. Harvey, S.C., M. Prabhakaran, B. Mao, J.A. McCammon. Phenylalanine Transfer RNA: Molecular Dynamics Simulation. Science 223, 1189-1191 (1984). [PubMed]
  48. McCammon, J.A. Protein Dynamics. Rep. Prog. Phys. 47, 1-46 (1984, Invited review).
  49. Northrup, S.H., J.A. McCammon. Gated Reactions. J. Amer. Chem. Soc. 106, 930-934 (1984).
  50. McCammon, J.A. Nucleic Acid Dynamics: Theoretical Methods for the Study of Long Timescale Processes. In "Report of the 1983 NATO/CECAM Workshop on Nucleic Acid Conformation/Dynamics," W. Olson, Ed., CECAM, Universite de Paris-Sud, pp. 98-101 (1984).
  51. Mao, B., J.A. McCammon. Structural Study of Hinge-bending in L-Arabinose-Binding Protein. J. Biol. Chem. 259, 4964-4970 (1984). [PubMed]
  52. Northrup, S.H., S.A. Allison, J.A. McCammon. Brownian Dynamics of Diffusion-Influenced Bimolecular Reactions. J. Chem. Phys. 80, 1517-1524 (1984).
  53. Tung, C.-S., S.C. Harvey, J.A. McCammon. Large-Amplitude Bending Motions in Phenylalanine Transfer RNA. Biopolymers 23, 2173-2193 (1984). [PubMed]
  54. Lee, C.-Y., J.A. McCammon, P.J. Rossky. The Structure of Liquid Water at an Extended Hydrophobic Surface. J. Chem. Phys. 80, 4448-4455 (1984).
  55. Berkowitz, M., O.A. Karim, J.A. McCammon, P.J. Rossky. Sodium Chloride Ion Pair Interaction in Water: Computer Simulation. Chem. Phys. Letters 105, 577-580 (1984).
  56. Tembe, B.L., J.A. McCammon. Ligand-Receptor Interactions. Comput. & Chem. 8, 281-283 (1984).
  57. Allison, S.A., N. Srinivasan, J.A. McCammon, S.H. Northrup. Diffusion-Controlled Reactions Between a Spherical Target and a Dumbell Dimer by Brownian Dynamics Simulation. J. Phys. Chem. 88, 6152-6157 (1984).

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