Molecular Mechanics Calculations of Proteins. Comparison of Different Energy Minimization Strategies

References and Footnotes

• Koehler , K. F. , Rao , S. N. and Snyder , J. P. 1996 . Guidebook on Molecular Modeling in Drug Design Edited by: Cohen , N. C. 235 – 336 . San Diego : Academic Press .
   Google Scholar
• Johnson , M. S. , Srinivasan , N. , Sowdhamini , R. and Blundell , T. L. 1994 . Crit. Rev. Biochem. Mol. Biol. , 29 : 1 – 68 .
   PubMed Web of Science ®Google Scholar
• Hutchins , C. and Greer , J. 1991 . Crit. Rev. Biochem. Molec. Biol. , 26 : 77 – 127 .
   PubMed Web of Science ®Google Scholar
• Shoichet , B. K. , Stroud , R. M. , Santi , D. V. , Kuntz , I. D. and Perry , K. M. 1993 . Science , 259 : 1445 – 1450 .
   PubMed Web of Science ®Google Scholar
• Walkinshaw , M. D. 1992 . Med. Res. Rev. , 12 : 317 – 372 .
   PubMed Web of Science ®Google Scholar
• Lam , P. Y. S. , Jadhav , P. K. , Eyermann , C. J. , Hodge , C. N. , Ru , Y. , Bacheler , L. T. , Meek , J. L. , Otto , M. J. , Rayner , M. M. , Wong , Y. N. , Chang , C. H. , Weber , P. C. , Jackson , D. A. , Sharpe , T. R. and Erickson-Viitanen , S. 1994 . Science , 263 : 380 – 384 .
   PubMed Web of Science ®Google Scholar
• Colman , P. M. 1994 . Curr. Opin. Struct. Biol. , 4 : 868 – 874 .
   PubMed Web of Science ®Google Scholar
• Whittle , P. J. and Blundell , T. L. 1994 . Annu. Rev. Biophys. Biomol. Struc. , 23 : 349 – 375 .
   PubMedGoogle Scholar
• Bohacek , R. S. , McMartin , C. and Guida , W. C. 1996 . Med. Res. Rev. , 16 : 3 – 50 .
   PubMed Web of Science ®Google Scholar
• Reich , S. H. and Webber , S. E. 1993 . Persp. Drug Discov. Des. , 1 : 371 – 390 .
   Google Scholar
• Bernstein , F. C. , Koetzle , T. F. , Williams , G. J. B. , Meyer , E. F. Jr , Brice , M. D. , Rodgers , J. R. , Kennard , O. , Shimanouchi , T. and Tasumi , M. 1977 . J. Mol. Biol. , 112 : 535 – 542 .
   PubMed Web of Science ®Google Scholar
• Hilbert , M. , Böhm , G. and Jaenicke , R. 1993 . Proteins , 17 : 138 – 151 .
   PubMed Web of Science ®Google Scholar
• Greer , J. , Erickson , J. W. , Baldwin , J. J. and Varney , M. D. 1994 . J. Med. Chem. , 37 : 1035 – 1054 .
   PubMed Web of Science ®Google Scholar
• Sali , A. 1995 . Curr. Opin. Biotech. , 6 : 437 – 451 .
   PubMed Web of Science ®Google Scholar
• Blundell , T. L. 1996 . Nature , 384 : 23 – 26 .
   PubMed Web of Science ®Google Scholar
• Appelt , K. , Bacquet , R. J. , Bartlett , C. A. , Booth , C. L. J. , Freer , S. T. , Fuhry , M. A. M. , Gehring , M. R. , Herrmann , S. M. , Howland , E. F. , Janson , C. A. , Jones , T. R. , Kan , C-C. , Kathardekar , V. , Lewis , K. K. , Marzoni , G. P. , Matthews , D. A. , Mohr , C. , Moomaw , E. W. , Morse , C. A. , Oatley , S. J. , Ogden , R. C. , Reddy , M. R. , Reich , S. H. , Schoettlin , W. S. , Smith , W. W. , Varney , M. D. , Villafranca , J. E. , Ward , R. W. , Webber , S. , Webber , S. E. , Welsh , K. M. and White , J. 1991 . J. Med. Chem. , 34 : 1925 – 1934 .
   PubMed Web of Science ®Google Scholar
• Goodsell , D. S. and Olson , A. J. 1990 . Proteins , 8 : 195 – 202 .
   PubMed Web of Science ®Google Scholar
• Leach , A. R. 1994 . J. Mol. Biol. , 235 : 345 – 356 .
   PubMed Web of Science ®Google Scholar
• Kuntz , I. D. , Meng , E. C. and Shoichet , B. K. 1994 . Acc. Chem. Res. , 27 : 117 – 123 .
   Web of Science ®Google Scholar
• Blaney , J. M. and Dixon , J. S. 1993 . Persp. Drug Discov. Des. , 1 : 301 – 319 .
   Google Scholar
• Straatsma , T. P. , Zacharias , M. and McCammon , J. A. 1993 . Computer Simulation of Biomolecular Systems. Theoretical and Experimental Applications. Vol. Edited by: van Gunsteren , W. F. , Weiner , P. K. and Wilkinson , A. J. Vol. 2 , 349 – 367 . Leiden : ESCOM Science Publishers B.V. . by
   Google Scholar
• Dijkstra , B. W. , Kalk , K. H. , Hol , W. G. J. and Drenth , J. 1981 . J. Mol. Biol. , 147 : 97 – 123 .
   PubMed Web of Science ®Google Scholar
• Blundell , T. L. , Pitts , J. E. , Tickle , I. J. , Wood , S. P. and Wu , C.-W. 1981 . Proc. Natl. Acad. Sci. USA. , 78 : 4175 – 4179 .
   PubMed Web of Science ®Google Scholar
• Fremont , D. H. , Anderson , D. H. , Wilson , I. A. , Dennis , E. A. and Xuong , N.-H. 1993 . Proc. Natl. Acad. Sci. USA , 90 : 342 – 346 .
   PubMed Web of Science ®Google Scholar
• Modin , C. R. , Christensen , I. T. and Jørgensen , F. S. in preparation
   Google Scholar
• Tripos Associates Inc., St. Louis, USA
   Google Scholar
• Labanowski , J. , Motoc , I. , Naylor , C. B. , Mayer , D. and Dammkoehler , R. A. 1986 . Quant. Struct.-Act. Relat. , 5 : 138 – 152 .
   Web of Science ®Google Scholar
• Clark , M. , Cramer , R. D. III and Van Opdenbosch , N. 1989 . J. Comput. Chem. , 10 : 982 – 1012 .
   Web of Science ®Google Scholar
• Weiner , S. J. , Kollman , P. A. , Nguyen , D. T. and Case , D. A. 1986 . J. Comput. Chem. , 7 : 230 – 252 .
   PubMed Web of Science ®Google Scholar
• Teeter , M. M. 1991 . Annu. Rev. Biophys. Biophys. Chem. , 20 : 577 – 600 .
   PubMedGoogle Scholar
• Blanco , M. 1991 . J. Comput. Chem. , 12 : 237 – 247 .
   Web of Science ®Google Scholar
• Stewart , J. J. P. 1990 . J. Comput.-Aided. Mol. Des. , 4 : 1 – 105 .
   PubMed Web of Science ®Google Scholar
• Pearlman , R. S. and Skell , J. M. SAVOL3: Numerical and Analytical Algorithms for Molecular Surface Area and Volume, software distributed by R. S. Pearlman 78712 Austin TX : College of Pharmacy, University of Texas .
   Google Scholar
• Morris , A. L. , MacArthur , M. W. , Hutchinson , E. G. and Thornton , J. M. 1992 . Proteins , 12 : 345 – 364 .
   PubMed Web of Science ®Google Scholar
• Kini , R. M. and Evans , H. J. 1991 . J. Biomol. Struct. Dyn. , 9 : 475 – 488 .
   PubMed Web of Science ®Google Scholar
• Shiratori , Y. and Nakagawa , S. 1991 . J. Comput. Chem. , 12 : 717 – 730 .
   Google Scholar
• Thrige , D. d. G. , Buur , J. R. B. and Jørgensen , F. S. 1997 . Biopolymers , 42 : 319 – 336 .
   PubMedGoogle Scholar
• Christensen , I. T. , Jørgensen , F. S. , Svensson , Å. L. and Högberg , T. 1993 . Drug Des. Discov. , 10 : 101 – 113 .
   PubMedGoogle Scholar
• Keith , C. , Feldman , D. S. , Deganello , S. , Glick , J. , Ward , K. B. , Jones , E. O. and Sigler , P. B. 1981 . J. Biol. Chem. , 256 : 8602 – 8607 .
   PubMed Web of Science ®Google Scholar
• Christensen , I. T. and Jørgensen , F. S. unpublished results
   Google Scholar
• Weiner , P. K. , Langridge , R. , Blaney , J. M. , Schaefer , R. and Kollman , P. A. 1982 . Proc. Natl. Acad. Sci. USA. , 79 : 3754 – 3758 .
   PubMed Web of Science ®Google Scholar
• von Freyberg , B. , Richmond , T. J. and Braun , W. 1993 . J. Mol. Biol. , 233 : 275 – 292 .
   PubMed Web of Science ®Google Scholar
• Still , W. C. , Tempczyk , A. , Hawley , R. C. and Hendrickson , T. F. 1990 . J. Am. Chem. Soc. , 112 : 6127 – 6129 .
   Web of Science ®Google Scholar
• Schiffer , C. A. , Caldwell , J. W. , Kollman , P. A. and Stroud , R. M. 1993 . Mol. Simul. , 102 : 121 – 149 .
   Google Scholar
• Stouten , P. F. W. , Frömmel , C. , Nakamura , H. and Sander , C. 1993 . Mol. Simul. , 102 : 97 – 120 .
   Google Scholar
• Scott , D. L. , White , S. P. , Otwinowski , Z. , Yuan , W. , Gelb , M. H. and Sigler , P. B. 1990 . Science , 250 : 1541 – 1546 .
   PubMed Web of Science ®Google Scholar
• Kraulis , P. J. 1991 . J. Appl. Cryst. , 24 : 946 – 950 .
   Web of Science ®Google Scholar