Molecular Modeling Course 99

A New Spring' 99 Offering


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SCIVIS Accounts
Chemistry: G25.2601
Biology: G23.2601
Mathematics: G63.2856.003
Computer Science: G22.3033.11
Sackler: G16.2607

Time: Thursdays, 12:45-2:45pm

Location: 1003 Main Building

Article Reading List

    Late 1950s

  1. B. J. Alder and T. E. Wainwright, Studies in Molecular Dynamics.I. General Method, J. Chem. Phys. 31, 459--466 (1959).


  2. G. Nemethy and H. A. Scheraga, Theoretical Determination of Sterically Allowed Conformations of a Polypeptide Chain by a Computer Method, Biopolymers 3, 155--184 (1965).


  3. A. Rahman and F. H. Stillinger, Molecular Dynamics Study of Liquid Water, J. Chem. Phys. 55, 3336--3359 (1971).

  4. P. Y. Chou and G. D. Fasman, Prediction of Protein Conformation, Biochemistry 13, 222--245 (1974).

  5. M. Levitt and A. Warshel, Computer Simulation of Protein Folding, Nature 253, 694--698 (1975).

  6. M. Levitt and C. Chothia, Structural Patterns in Globular Proteins, Nature 261, 552--558 (1976).


  7. S. Lifson, Potential Energy Functions for Structural Molecular Biology, Methods in Structural Molecular Biology pp. 359--385, D. B. Davies, W. Saenger, and S. S. Danyluk, Eds., Plenum Press, London (1981).

  8. M. Karplus and J. A. McCammon, The Dynamics of Proteins, Sci. Amer. 254, 42--51 (1986).

  9. M. S. Friedrichs and P. G. Wolynes, Toward Protein Tertiary Structure Recognition by Means of Associative Memory Hamiltonians, Science 246, 371--373 (1989).

  10. I. K. Roterman, M. H. Lambert, K. D. Gibson, and H. A. Scheraga, Comparison of the CHARMM, AMBER and ECEPP Potentials for Peptides. I. Conformational Predictions for the Tandemly Repeated Peptide (Asn-Ala-Asn-Pro)9, J. Biomol. Struct. Dyn. 7, 391--419 (1989a).

  11. I. K. Roterman, M. H. Lambert, K. D. Gibson, and H. A. Scheraga, Comparison of the CHARMM, AMBER and ECEPP Potentials for Peptides. II. phi-psi Maps for NMethyl Amide: Comparisons, Contrasts and Simple Experimental Tests, J. Biomol. Struct. Dyn. 7, 421--453 (1989b).


  12. M. Karplus and G. A. Petsko, Molecular Dynamics Simulations in Biology, Nature 347, 631--639 (1990).

  13. J. Skolnick and A. Kolinski, Simulations of the Folding of a Globular Protein, Science 250, 1121--1125 (1990).

  14. F. M. Richards, The Protein Folding Problem, Sci. Amer. 264, 54--63 (1991).

  15. P. A. Kollman and K. A. Dill, Decisions in Force Field Development: An Alternative to Those Described by Roterman et al., J. Biomol. Struct. Dyn. 8, 1103--1107 (1991).

  16. K. B. Gibson and H. A. Scheraga, Decisions in Force Field Development: Reply to Kollman and Dill, J. Biomol. Struct. Dyn. 8, 1109--1111 (1991).

  17. H. A. Scheraga, Predicting Three-Dimensional Structures of Oligopeptides, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Editors, Vol. 3, pp. 73--142, VCH Publishers, New York (1992).

  18. T. Schlick, Optimization Methods in Computational Chemistry, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Editors, Vol. 3, pp. 1--71, VCH Publishers, New York (1992).


  19. R. A. Abagyan and M. M. Totrov, Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins, J. Mol. Biol. 235, 983--1002 (1994).

  20. J. A. Board, Jr., L. V. Kale, K. Schulten, R. D. Skeel, and T. Schlick, Modeling Biomolecules: Larger Scales, Longer Durations, IEEE Comp. Sci. Eng. 1, 19--30 (Winter 1994).

  21. K. B. Lipkowitz, Abuses of Molecular Mechanics. Pitfalls to Avoid, J. Chem. Educ. 72, 1070--1075 (1995).

  22. B. Honig and A. Nicholls, Classical Electrostatics in Biology and Chemistry, Science 268, 1144--1149 (1995).


  23. B. Cipra, Computer Science Discovers DNA, What's Happening in the Mathematical Sciences, pp. 26--37 (P. Zorn, Ed.), American Mathematical Society, Colonial Printing, Cranston, RI (1996).

  24. A. Neumaier, Molecular Modeling of Proteins and Mathematical Prediction of Protein Structure, SIAM Review 39, 407--460 (1997).

  25. K. A. Dill and H. S. Chan, From Levinthal to Pathways to Funnels, Nature Struc. Biol. 4, 10--19 (1997).

  26. T. Lazaridis and M. Karplus, New View of Protein Folding Reconciled with the Old Through Multiple Unfolding Simulations Science 278, 1928--1931 (1997).

  27. T. Schlick, E. Barth, and M. Mandziuk, Biomolecular Dynamics at Long Timesteps: Bridging the Timescale Gap Between Simulation and Experimentation, Ann. Rev. Biophys. Biomol. Struc. 26, 179--220 (1997).

  28. E. Barth and T. Schlick, Overcoming Stability Limitations in Biomolecular Dynamics: I. Combining Force Splitting via Extrapolation with Langevin Dynamics in LN, J. Chem. Phys. 109, 1617--1632 (1998).

  29. M. Gerstein and M. Levitt, Simulating Water and the Molecules of Life, Sci. Amer. 279, 101--105 (1998).

  30. Y. Duan and P. A. Kollman, Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution, Science 282, 740--744 (1998).

  31. H. J. C. Berendsen, A Glimpse of the Holy Grail, Science 282, 642--643 (1998).

  32. L. S. D. Caves, J. D. Evanseck, and M. Karplus, Locally Accessible Conformations of Proteins: Multiple Molecular Dynamics Simulations of Crambin, Prot. Sci. 7, 649--666 (1998).

  33. W. F. van Gunsteren and A. E. Mark, Validation of Molecular Dynamics Simulation, J. Chem. Phys. 108, 6109--6116 (1998).

  34. X. Daura, B. Juan, D. Seebach, W. F. Van Gunsteren, and A. Mark, Reversible Peptide Folding in Solution by Molecular Dynamics Simulation, J. Mol. Biol. 280, 925--932 (1998).


For further information, contact T. Schlick by email ( phone (998-3116) or fax (995-4152).