manual.14.html
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML EXPERIMENTAL 970324//EN"><HTML><HEAD><META NAME="GENERATOR" CONTENT="Adobe FrameMaker 5.5/HTML Export Filter"><LINK REL="STYLESHEET" HREF="Manual.css"><TITLE> References</TITLE></HEAD><BODY BGCOLOR="#ffffff"><H2 CLASS="Heading-2"><A NAME="pgfId=4569"> </A><A NAME="marker=4568"> </A><A NAME="29403"> </A>References</H2><OL><LI CLASS="Reference"><A NAME="pgfId=10300"> </A>1. Blaney, J.M. Ph.D. dissertation, University of California, San Francisco, 1982.</LI><LI CLASS="Reference"><A NAME="pgfId=4572"> </A>2. Connolly, M.L. Analytical molecular surface calculation. J. Appl. Cryst. 16: 548-558, 1983.</LI><LI CLASS="Reference"><A NAME="pgfId=4573"> </A>3. Connolly, M.L. Solvent-accessible surfaces of proteins and nucleic acids. Science. 221: 709-713, 1983.</LI><LI CLASS="Reference"><A NAME="pgfId=9858"> </A>4. <A NAME="13890"> </A>DesJarlais, R.L., and Dixon, J.S. A shape and chemistry-based docking method and its use in the design of HIV-1 protease inhibitors. J. Comput.-Aided Molec. Design 8(3): 231-242, 1994.</LI><LI CLASS="Reference"><A NAME="pgfId=4574"> </A>5. DesJarlais, R.L., Sheridan, R.P., Seibel, G.L., Dixon, J.S., Kuntz, I.D. and Venkataraghavan, R. Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure. J. Med. Chem. 31(4): 722-729, 1988.</LI><LI CLASS="Reference"><A NAME="pgfId=4575"> </A>6. <A NAME="13035"> </A>Ewing, T.J.A, and Kuntz, I.D. Critical evaluation of search algorithms used in automated molecular docking. J. Comput. Chem. 18(9): 1175-1189, 1997.</LI><LI CLASS="Reference"><A NAME="pgfId=8396"> </A>7. Ferro, D.R. and Hermans, J. A different best rigid-body molecular fit routine. Acta Cryst. A33: 345-347, 1977.</LI><LI CLASS="Reference"><A NAME="pgfId=4576"> </A>8. Fletcher, R. "Practical Methods of Optimization." New York: Interscience, 1960.</LI><LI CLASS="Reference"><A NAME="pgfId=4577"> </A>9. Gilson, M.K., Sharp, K.A. and Honig, B.H. J. Comp. Chem. 9: 327, 1987.</LI><LI CLASS="Reference"><A NAME="pgfId=4578"> </A>10. Goodford, P.J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 28: 849-857, 1985.</LI><LI CLASS="Reference"><A NAME="pgfId=8794"> </A>11. <A NAME="38078"> </A>Gschwend, D.A, and Kuntz, I.D. Orientational sampling and rigid-body minimization in molecular docking revisited -- On-the-fly optimization and degeneracy removal. J. Comput.-Aided Molec. Design, 10:123-132, 1996.</LI><LI CLASS="Reference"><A NAME="pgfId=4579"> </A>12. Kabsch, W. A solution for the best rotation to relate two sets of vectors. Acta Cryst. A32: 922-923, 1976.</LI><LI CLASS="Reference"><A NAME="pgfId=4580"> </A>13. Kabsch, W. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Cryst. 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Res. 27(5): 117-123, 1994.</LI><LI CLASS="Reference"><A NAME="pgfId=10020"> </A>19. <A NAME="30470"> </A>Leach, A.R., and Kuntz, I.D. Conformational analysis of flexible ligands in macromolecular receptor sites. J. Comput. Chem. 13(6): 730-748, 1992.</LI><LI CLASS="Reference"><A NAME="pgfId=4585"> </A>20. <A NAME="17773"> </A>Meng, E.C., Shoichet, B.K. and Kuntz, I.D. Automated docking with grid-based energy evaluation. J. Comp. Chem. 13: 505-524, 1992.</LI><LI CLASS="Reference"><A NAME="pgfId=4586"> </A>21. Meng, E.C., Gschwend, D.A., Blaney, J.M. and Kuntz, I.D. Orientational sampling and rigid-body minimization in molecular docking. Proteins. 17(3): 266-278, 1993.</LI><LI CLASS="Reference"><A NAME="pgfId=4587"> </A>22. Meng, E.C., Kuntz, I.D., Abraham, D.J. and Kellogg, G.E. Evaluating docked complexes with the hint exponential function and empirical atomic hydrophobicities. J. Comp-Aided Mol. Design. 8: 299-306, 1994.</LI><LI CLASS="Reference"><A NAME="pgfId=9861"> </A>23. <A NAME="64587"> </A>Miller, M.D., Kearsley, S.K., Underwood, D.J. and Sheridan, R.P. FLOG - A system to select quasi-flexible ligands complementary to a receptor of known three-dimensional structure. J. Comput.-Aided Mol. Design </LI><LI CLASS="Reference"><A NAME="pgfId=4588"> </A>24. Nelder, J.A. and Mead, R. Computer Journal 7: 308, (1965).</LI><LI CLASS="Reference"><A NAME="pgfId=4589"> </A>25. Richards, F.M. Ann. Rev. Biophys. Bioeng. 6: 151-176, 1977.</LI><LI CLASS="Reference"><A NAME="pgfId=4590"> </A>26. <A NAME="22657"> </A>Shoichet, B.K. and Kuntz, I.D. Protein docking and complementarity. J. Mol. Biol. 221: 327-346, 1991.</LI><LI CLASS="Reference"><A NAME="pgfId=4591"> </A>27. Shoichet, B.K., Bodian, D.L. and Kuntz, I.D. Molecular docking using shape descriptors. J. Comp. Chem. 13(3): 380-397, 1992.</LI><LI CLASS="Reference"><A NAME="pgfId=4592"> </A>28. Shoichet, B.K., Stroud, R.M., Santi, D.V., Kuntz, I.D. and Perry, K.M. Structure-based discovery of inhibitors of thymidylate synthase. Science. 259: 1445-1450, 1993.</LI><LI CLASS="Reference"><A NAME="pgfId=4593"> </A>29. Shoichet, B.K. and Kuntz, I.D. Matching chemistry and shape in molecular docking. Protein Eng. 6(7): 723-732, 1993.</LI><LI CLASS="Reference"><A NAME="pgfId=4594"> </A>30. Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta, S., Jr. and Weiner, P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106: 765-784, 1984.</LI><LI CLASS="Reference"><A NAME="pgfId=4595"> </A>31. Weiner, S.J., Kollman, P.A., Nguyen, D.T. and Case, D.A. An all atom force field for simulations of proteins and nucleic acids. J. Comp. Chem. 7: 230-252, 1986.</LI></OL><P CLASS="Normal"><A NAME="pgfId=488"> </A> </P><CENTER><P>⌨️ 快捷键说明
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