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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
- B. J. Alder and T. E. Wainwright,
Studies in Molecular Dynamics.I. General Method,
J. Chem. Phys. 31, 459--466 (1959).
1960s
- 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).
1970s
- A. Rahman and F. H. Stillinger, Molecular Dynamics Study of Liquid Water, J. Chem. Phys. 55, 3336--3359 (1971).
- P. Y. Chou and G. D. Fasman,
Prediction of Protein Conformation,
Biochemistry 13, 222--245 (1974).
- M. Levitt and A. Warshel,
Computer Simulation of Protein Folding,
Nature 253, 694--698 (1975).
- M. Levitt and C. Chothia,
Structural Patterns in Globular Proteins,
Nature 261, 552--558 (1976).
1980s
- 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).
- M. Karplus and J. A. McCammon,
The Dynamics of Proteins,
Sci. Amer. 254, 42--51 (1986).
- M. S. Friedrichs and P. G. Wolynes,
Toward Protein Tertiary Structure Recognition by Means of Associative Memory
Hamiltonians,
Science 246, 371--373 (1989).
- 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).
- 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).
1990-1992
- M. Karplus and G. A. Petsko,
Molecular Dynamics Simulations in Biology,
Nature 347, 631--639 (1990).
- J. Skolnick and A. Kolinski,
Simulations of the Folding of a Globular Protein,
Science 250, 1121--1125 (1990).
- F. M. Richards,
The Protein Folding Problem,
Sci. Amer. 264, 54--63 (1991).
- 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).
- 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).
- 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).
- 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).
1993-1995
- 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).
- 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).
- K. B. Lipkowitz,
Abuses of Molecular Mechanics. Pitfalls to Avoid,
J. Chem. Educ.
72, 1070--1075 (1995).
- B. Honig and A. Nicholls,
Classical Electrostatics in Biology and Chemistry,
Science
268, 1144--1149 (1995).
1996--
- 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).
- A. Neumaier,
Molecular Modeling of Proteins and Mathematical Prediction
of Protein Structure,
SIAM Review
39, 407--460 (1997).
- K. A. Dill and H. S. Chan,
From Levinthal to Pathways to Funnels,
Nature Struc. Biol. 4, 10--19 (1997).
- T. Lazaridis and M. Karplus,
New View of Protein Folding Reconciled with the Old Through
Multiple Unfolding Simulations
Science
278, 1928--1931 (1997).
- 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).
- 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).
- M. Gerstein and M. Levitt,
Simulating Water and the Molecules of Life,
Sci. Amer. 279, 101--105 (1998).
- 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).
- H. J. C. Berendsen,
A Glimpse of the Holy Grail,
Science
282, 642--643 (1998).
- 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).
- W. F. van Gunsteren and A. E. Mark,
Validation of Molecular Dynamics Simulation,
J. Chem. Phys. 108, 6109--6116 (1998).
- 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).
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