An Internal Coordinate Monte Carlo Method for Searching Conformational Space

Journal of the American Chemical Society

Volumn 111, Issue 12, 1989, Pages 4379-4386

  Chang, George ^a   Guida, Wayne C ^b   Still, W Clark ^a  

^a Columbia University ^*  (United States)

^b CIBA GEIGY Corporation ^*  (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0043162336     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja00194a035     Document Type: Article

References (12)

1. Review: Howard, A. E.; Kollman, P. A. J. Med. Chem. 1988, 31, 1669.
2. Lipton, M.; Still, W. C. J. Comp. Chem. 1988, 9, 343. (b) Bruccoleri, R.; Karplus, M. Biopolymers 1987, 26, 137. (c) Motoc, I.; Dammkoehler, R. A.; Mayer, D.; Labanowski, J. Quant. Struct.—Act. Relat. 1986, 5, 99. (d) Fukazawa, Y.; Usui, S.; Uchio, Y.; Shiobara, Y. and Kodama, M. Tetrahedron Lett. 1986, 27, 1825. (e) White, D. N. J.; Kitson, D. H. J. Mol. Graphics 1986, 4, 112. (f) Smith, G. M.; Weber, D. F. Biochem. Biophys. Res. Commun. 1986, 134, 907. (g) Dyert, M.; Go, N.; Scheraga, H. A. Macromolecules 1975, 8, 750. (h) Noguti, T.; Go, N. Biopolymers 1985, 24, 527. (i) Fine, R. M.; Wang, H.; Shenkin, P. S.; Yarmush, D. L.; Levinthal, C. Proteins: Struct. Funct. Genet. 1986, 1, 342. (j) Still, W. C.; Galynker, I. Tetrahedron 1981, 37, 3981.
3. Saunders, M. J. Am. Chem. Soc. 1987, 109, 3150. (b) We wish to thank Professor Douglas Raber of the University of South Florida for a preprint describing his random Cartesian search method (the preceding paper in this issue).
4. Crippen, G. Distance Geometry and Conformational Calculations; Research Studies Press, Wiley: New York, 1981. (b) Weiner, P. K.; Profeta, S.; Wipff, G.; Havel, T.; Kuntz, 1. D.; Langridge, R.; Kollman, P. A. Tetrahedron 1983, 39, 1113.
5. Brooks, B. R. Proceedings from Supercomputer Research in Chemistry and Chemical Engineering: Truhlar, D., Jensen, K., Eds.; American Chemical Society: Washington, DC, 1987. Brown, F. K.; Kollman, P. A. J. Mol. Biol. 1987, 198, 533. Fesik, S. W.; O'Donnell, T. J.; Gampe, R. T.; Olejniczak, E. T. J. Am. Chem. Soc. 1986, 108, 3165. Brunger, A. T.; Clore, G. M.; Gronenborn, A. M., Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 3801.
6. Loncharich, R. J.; Seward, E.; Ferguson, S. B.; Brown, F. K.; Diederich, F.; Houk, K. N. J. Org. Chem. 1988, 53, 3479. (b) Billeter, M.; Havel, T. F.; Wuthrich, K. J. Comput. Chem. 1987, 8, 132. (c) Shor, N. Z. Cybernetics 1977, 12, 94.
7. Li, Z.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 6611. See also: Wilson, S. R.; Cui, W.; Moscowitz, J. W.; Schmidt, K. E. Tetrahedron Lett. 1988, 29, 4373.
8. Batchmin is part of the MacroModel molecular modeling program: Still, W. C.; Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; CauField, C.; Chang, G.; Hendrickson, T. MacroModel V2.0; Department of Chemistry, Columbia University; New York.
9. Kabsh, W. Acta Crystallogr. 1976, A32, 944. Kabsh, W. Acta Crystallogr. 1978, A34, 827.
10. We used Allinger MM2 force field (Allinger, N. L. J. Am. Chem. Soc. 1977, 99, 8127 for all the calculations on hydrocarbons. For functionalized molecules, the MacroModel implementation of MM2 uses a partial charge treatment for electrostatics and the calculations described employed a distance-dependent (e = R) dielectric.
11. Weber, H. P.; Hauser, D.; Sigg, A. P. Helv. Chem. Acta 1971, 54, 2263.
12. Hutchinson, C. R.; Kurobane, I.; Cane, D. E.; Hasler, H.; McInnes, A. G. J. Am. Chem. Soc. 1981, 103, 2477.