Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions

Journal of Computational Chemistry

Volumn 32, Issue 8, 2011, Pages 1680-1686

  Liang, Shide ^a   Zhou, Yaoqi ^b,c   Grishin, Nick ^d   Standley, Daron M ^a  

^a OSAKA UNIVERSITY   (Japan)

^b INDIANA UNIVERSITY   (United States)

^c INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

Monte Carlo simulation; orientation dependent force fields; parameter optimization; series expansions; side chain modeling

Indexed keywords

MONTE CARLO SIMULATION; ORIENTATION DEPENDENT; PARAMETER OPTIMIZATION; SERIES EXPANSION; SIDE CHAIN MODELING;

COMPUTER SIMULATION; CONFORMATIONS; CRYSTAL STRUCTURE; DIHEDRAL ANGLE; EXPANSION; FOURIER ANALYSIS; FOURIER SERIES; HARMONIC ANALYSIS; MONTE CARLO METHODS; POTENTIAL ENERGY FUNCTIONS; PROTEINS;

OPTIMIZATION;

PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; INTERNET; PROTEIN CONFORMATION;

INTERNET; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SOFTWARE;

EID: 79953753344     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21747     Document Type: Article

References (34)

1. Baker, D.,;, Sali, A., Science 2001, 294, 93.
2. Zhang, Y., Curr Opin Struct Biol 2008, 18, 342.
3. Dunbrack, R. L., Jr., Curr Opin Struct Biol 2006, 16, 374.
4. Qian, B.,;, Ortiz, A. R.,;, Baker, D., Proc Natl Acad Sci USA 2004, 101, 15346.
5. MacCallum, J. L.,;, Hua, L.,;, Schnieders, M. J.,;, Pande, V. S.,;, Jacobson, M. P.,;, Dill, K. A., Proteins 2009, 77 (Suppl 9), 66.
6. MacKerell, A. D.,;, Bashford, D.,;, Bellott, M.,;, Dunbrack, R. L.,;, Evanseck, J. D.,;, Field, M. J.,;, Fischer, S.,;, Gao, J.,;, Guo, H.,;, Ha, S.,;, Joseph-McCarthy, D.,;, Kuchnir, L.,;, Kuczera, K.,;, Lau, F. T. K.,;, Mattos, C.,;, Michnick, S.,;, Ngo, T.,;, Nguyen, D. T.,;, Prodhom, B.,;, Reiher, W. E.,;, Roux, B.,;, Schlenkrich, M.,;, Smith, J. C.,;, Stote, R.,;, Straub, J.,;, Watanabe, M.,;, Wiorkiewicz-Kuczera, J.,;, Yin, D.,;, Karplus, M., J Phys Chem B 1998, 102, 3586.
7. Cornell, W. D.,;, Cieplak, P.,;, Bayly, C. I.,;, Gould, I. R.,;, Merz, K. M.,;, Ferguson, D. M.,;, Spellmeyer, D. C.,;, Fox, T.,;, Caldwell, J. W.,;, Kollman, P. A., J Am Chem Soc 1996, 118, 2309.
8. Scott, W. R. P.,;, Hunenberger, P. H.,;, Tironi, I. G.,;, Mark, A. E.,;, Billeter, S. R.,;, Fennen, J.,;, Torda, A. E.,;, Huber, T.,;, Kruger, P.,;, van Gunsteren, W. F., J Phys Chem A 1999, 103, 3596.
9. Lu, M.,;, Dousis, A. D.,;, Ma, J., J Mol Biol 2008, 376, 288.
10. Majek, P.,;, Elber, R., Proteins 2009, 76, 822.
11. Miyazawa, S.,;, Jernigan, R. L., Macromolecules 1985, 18, 534.
12. Rata, I. A.,;, Li, Y.,;, Jakobsson, E., J Phys Chem B, 114, 1859.
13. Shen, M. Y.,;, Sali, A., Protein Sci 2006, 15, 2507.
14. Zhou, H.,;, Zhou, Y., Protein Sci 2002, 11, 2714.
15. Yang, Y. D.,;, Zhou, Y. Q., Proteins 2008, 72, 793.
16. Huang, S. Y.,;, Zou, X., Proteins 2008, 72, 557.
17. Chiu, T. L.,;, Goldstein, R. A., Fold Des 1998, 3, 223.
18. Thomas, P. D.,;, Dill, K. A., Proc Natl Acad Sci USA 1996, 93, 11628.
19. Bastolla, U.,;, Vendruscolo, M.,;, Knapp, E. W., Proc Natl Acad Sci USA 2000, 97, 3977.
20. Winther, O.,;, Krogh, A., Phys Rev E Stat Nonlin Soft Matter Phys 2004, 70 (3 Pt 1), 030903.
21. Soto, C. S.,;, Fasnacht, M.,;, Zhu, J.,;, Forrest, L.,;, Honig, B., Proteins 2008, 70, 834.
22. Kuhlman, B.,;, Baker, D., Proc Natl Acad Sci USA 2000, 97, 10383.
23. Liang, S.,;, Grishin, N. V., Protein Sci 2002, 11, 322.
24. Löwdin, P.-O.,; Advances in quantum chemistry. Academic Press: New York, 1964.
25. Miyazawa, S.,;, Jernigan, R. L., J Chem Phys 2005, 122,024901
26. Word, J. M.,;, Lovell, S. C.,;, Richardson, J. S.,;, Richardson, D. C., J Mol Biol 1999, 285, 1735.
27. Dunbrack, R. L., Jr.,;, Cohen, F. E., Protein Sci 1997, 6, 1661.
28. Engh, R. A.,;, Huber, R., Acta Crystallogr Sect A 1991, 47, 392.
29. Liang, S. D.,;, Grishin, N. V., Proteins 2004, 54, 271.
30. Wilson, C.,;, Gregoret, L. M.,;, Agard, D. A., J Mol Biol 1993, 229, 996.
31. Petrella, R. J.,;, Lazaridis, T.,;, Karplus, M., Fold Des 1998, 3, 588.
32. Peterson, R. W.,;, Dutton, P. L.,;, Wand, A. J., Protein Sci 2004, 13, 735.
33. Lu, M. Y.,;, Dousis, A. D.,;, Ma, J. P., Protein Sci 2008, 17, 1576.
34. Krivov, G. G.,;, Shapovalov, M. V.,;, Dunbrack, R. L., Jr., Proteins 2009, 77, 778.