Download Annual Review of Pharmacology and Toxicology: 2003 by Arthur K. Cho, Terrence F. Blaschke, Paul A. Insel, Horace PDF

By Arthur K. Cho, Terrence F. Blaschke, Paul A. Insel, Horace H. Loh

ISBN-10: 0824304438

ISBN-13: 9780824304430

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Extra info for Annual Review of Pharmacology and Toxicology: 2003

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Combining Explicit and Implicit Solvent Models Recently, explicit and implicit solvent models have been combined to facilitate free energy calculations (36–40). This approach uses explicit solvent molecular dynamics simulations to relax crystal structures to solution ones, and then uses the simulated solution structures in implicit-solvent calculations to obtain free energy. Using implicit-solvent models eliminates the extensive simulation time required for sampling solvent configurations. This approach assumes that the free energy of a system can be obtained by averaging the potential of mean force, obtained from an implicit solvent model, of dynamics snapshots generated from explicit-solvent models.

1986. Free energy simulations. Ann. Acad. Sci. NY 482: 1–23 6. Bash PA, Singh UC, Langridge R, Kollman PA. 1987. Free energy calculation by computer simulation. Science 236:564–68 7. Jorgensen WL. 1989. Free energy calculations: a breakthrough for modeling organic chemistry in solution. Acc. Chem. Res. 22:184–89 8. Beveridge DL, DiCapua FM. 1989. Free energy via molecular simulation: applications to chemical and biomolecular systems. Annu. Rev. Biophys. Biophys. Chem. 18:431–92 9. Zwanzig RW. 1954.

Chem. 95:8585–97 Wong CF. 1991. Systematic sensitivity analyses in free energy perturbation calculations. J. Am. Chem. Soc. 113:3208–9 Wong CF, Rabitz H. 1991. Sensitivity analysis and principal component analysis in free energy calculations. J. Phys. Chem. 95:9628–30 Zhu S-B, Wong CF. 1993. sgm LaTeX2e(2002/01/18) PROTEIN FLEXIBILITY AND DRUG DESIGN 23. 24. 25. 26. 27. 28. 29. 30. 31. 32. 33. 34. analysis of distribution functions of liquid water. J. Chem. Phys. 99:9047–53 Zhu S-B, Wong CF. 1993.

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