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NYU CSCI-GA 3033 - Article Reading List

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This is page 3Printer: Opaque thisArticle Reading ListBefore 19701. B. J. Alder and T. E. Wainwright, “Studies in Molecular Dynamics. I. GeneralMethod”, J. Chem. Phys. 31, 459–466 (1959).2. G. N´emethy and H. A. Scheraga, “Theoretical Determination of Sterically AllowedConformations of a Polypeptide Chain by a Computer Method”, Biopolymers 3,155–184 (1965).1970s3. 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”, Biochemistry13, 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).1980s7. S. Lifson, “Potential Energy Functions for Structural Molecular Biology”, in Meth-ods in Structural Molecular Biology, pp. 359–385, D. B. Davies, W. Saenger, andS. 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 Recognitionby Means of Associative Memory Hamiltonians”, Science 246, 371–373 (1989).10. I. K. Roterman, M. H. Lambert, K. D. Gibson, and H. A. Scheraga, “Comparisonof the CHARMM, AMBER and ECEPP Potentials for Peptides. I. ConformationalPredictions for the Tandemly Repeated Peptide (Asn-Ala-Asn-Pro)”, J. Biomol.Struct. Dyn. 7, 391–419 (1989a).11. I. K. Roterman, M. H. Lambert, K. D. Gibson, and H. A. Scheraga, “Compari-son of the CHARMM, AMBER and ECEPP Potentials for Peptides. II.– Maps4 2. Article Reading Listfor N´-Methyl Amide: Comparisons, Contrasts and Simple Experimental Tests”, J.Biomol. Struct. Dyn. 7, 421–453 (1989b).1990–199212. 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 Alterna-tive 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: Replyto Kollman and Dill”, J. Biomol. Struct. Dyn. 8, 1109–1111 (1991).17. H. A. Scheraga, “Predicting Three-Dimensional Structures of Oligopeptides”, inReviews 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 inComputational Chemistry, K. B. Lipkowitz and D. B. Boyd, Editors, Vol. 3, pp.1–71, VCH Publishers, New York (1992). See also T. Schlick, “Geometry Opti-mization”, in the Encyclopedia of Computational Chemistry, P. von Ragu´e Schleyer(Editor-in-Chief) and N. L. Allinger and T. Clark and J. Gasteiger and P. A. Koll-man and Schaefer, III, H. F., Editors, Vol. 3, pp. 1136–1157, John Wiley & Sons,West Sussex, UK (1998).1993–199519. R. A. Abagyan and M. M. Totrov, “Biased Probability Monte Carlo ConformationalSearches and Electrostatic Calculations for Peptides and Proteins”, J. Mol. Biol.235, 983–1002 (1994).20. J. A. Board, Jr., L. V. Kal´e, K. Schulten, R. D. Skeel, and T. Schlick, “ModelingBiomolecules: 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).1996–199823. B. Cipra, “Computer Science Discovers DNA”, in What’s Happening in the Math-ematical 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 ofProtein Structure”, SIAM Review 39, 407–460 (1997).2. Article Reading List 525. 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 theOld Through Multiple Unfolding Simulations”, Science 278, 1928–1931 (1997).27. T. Schlick, E. Barth, and M. Mandziuk, “Biomolecular Dynamics at Long Time-steps: 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 Dy-namics: I. Combining Force Splitting via Extrapolation with Langevin Dynamics inLN”, J. Chem. Phys. 109, 1617–1632 (1998).29. M. Gerstein and M. Levitt, “SimulatingWater and the Molecules ofLife”, Sci. Amer.279, 101–105 (1998).30. Y. Duan and P. A. Kollman, “Pathways to a Protein Folding Intermediate Observedin 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 Conformationsof 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 DynamicsSimulation”, J. Chem. Phys. 108, 6109–6116 (1998).34. X. Daura, B. Juan, D. Seebach, W. F. Van Gunsteren, and A. Mark, “ReversiblePeptide Folding in Solution by Molecular Dynamics Simulation”, J. Mol. Biol. 280,925–932 (1998).1999–35. D. Baker and A. Sali, “Protein Structure Prediction and Structural Genomics”,Science 294, 93–96


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