Energy minimizations with a combination of two knowledge-based potentials for protein folding

Journal of Computational Chemistry

Volumn 29, Issue 10, 2008, Pages 1684-1692

  De Sancho, David ^a,b   Rey, Antonio ^a  

^a UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

^b CENTRO DE INVESTIGACIONES BIOLÓGICAS   (Spain)

Author keywords

Coarse grained models; Genetic algorithms; Molecular modeling; Protein structure

Indexed keywords

COMPLEXATION; FLOW INTERACTIONS; HYDROGEN; HYDROGEN BONDS; KNOWLEDGE BASED SYSTEMS; OPTIMIZATION;

COARSE GRAINED (CG); COMPUTATIONALLY EFFICIENT; DIFFERENT TYPES; ENERGY MINIMIZATIONS; EVOLUTIONARY METHODS; FOLDING PROCESSES; FORCE FIELD (FF); GLOBAL ENERGY; KNOWLEDGE-BASED; MOLECULAR SIMULATIONS; PROTEIN STRUCTURES; SIDE CHAIN INTERACTIONS;

PROTEIN FOLDING;

PROTEIN;

ALGORITHM; ARTICLE; CHEMICAL MODEL; CHEMISTRY; HYDROGEN BOND; PROTEIN FOLDING; THERMODYNAMICS;

ALGORITHMS; HYDROGEN BONDING; MODELS, CHEMICAL; PROTEIN FOLDING; PROTEINS; THERMODYNAMICS;

EID: 46449085241     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20924     Document Type: Article

References (44)

1. Skolnick, J. Curr Opin Struc Biol 2006, 16, 166.
2. Dill, K. A.; Bromberg, S.; Yue, K.; Fiebig, K. M.; Yee, D. P.; Thomas, P. D.; Chan, H. S. Protein Sci 1995, 4, 561.
3. Tozzini, V. Curr Opin Struc Biol 2005, 15, 144.
4. Ponder, J. W.; Case, D. A. Adv Protein Chem 2003, 66, 27.
5. Deshpande, N.; Addess, K. J.; Bluhm, W. F.; Merino-Ott, J. C.; Townsend-Merino, W.; Zhang, Q.; Knezevich, C.; Xie, L.; Chen, L.; Feng, Z.; Green, R. K.; Flippen-Anderson, J. L.; Westbrook, J.; Berman, H. M.; Bourne, P. E., Nucleic Acids Res 2005, 33, D233.
6. Sippl, M. J. J Mol Biol 1990, 213, 859.
7. Buchete, N.; Straub, J.; Thirumalai, D. Curr Opin Struc Biol 2004, 14, 225.
8. Jernigan, R. L.; Bahar, I. Curr Opin Struc Biol 1996, 6, 195.
9. Miyazawa, S.; Jernigan, R. L. J Mol Biol 1996, 256, 623.
10. Samudrala, R.; Moult, J. J Mol Biol 1998, 275, 895.
11. Lu, H.; Skolnick, J. Proteins 2001, 44, 223.
12. Zhou, H.; Zhou, Y. Protein Sci 2002, 11, 2714.
13. Shen, M. Y.; Sali, A. Protein Sci 2006, 15, 2507.
14. De Sancho, D.; Rey, A. J Chem Phys 2006, 125, 014904.
15. Tobi, D.; Shafran, G.; Linial, N.; Elber, R. Proteins 2000, 40, 71.
16. Nanias, M.; Chinchio, M.; Pillardy, J.; Ripoll, D. R.; Scheraga, H. A. Proc Natl Acad Sci USA 2003, 100, 1706.
17. Zhang, C.; Liu, S.; Zhou, H.; Zhou, Y. Protein Sci 2004, 13, 400.
18. Liu, S.; Zhang, C.; Zhou, H.; Zhou, Y. Proteins 2004, 56, 93.
19. Zhou, Y.; Zhou, H.; Zhang, C.; Liu, S. Cell Biochem Biophys 2006, 46, 165.
20. Zhou, H.; Zhou, Y. Proteins 2004, 54, 315.
21. Zhang, C.; Liu, S.; Zhu, Q.; Zhou, Y. J Med Chem 2005, 48, 2325.
22. Zhang, C.; Liu, S.; Zhou, Y. Proteins, 2005, 60, 314.
23. Pandey, B.; Zhang, C.; Yuan, X.; Zi, J.; Zhou, Y. Protein Sci 2005, 14, 1772.
24. Li, H.; Zhou, Y. J Bioinfo Comput Biol 2005, 3, 1151.
25. Zhou, H.; Xue, B.; Zhou, Y. Protein Sci 2007, 16, 947.
26. Larriva, M.; de Sancho, D.; Rey, A. Phys A 2006, 371, 449.
27. De Sancho, D.; Rey, A. J Comput Chem 2007, 28, 1187.
28. Kolinski, A. Acta Biochim Polym 2004, 51, 349.
29. Ekonomiuk, D.; Kielbasinski, M.; Kolinski, A. Acta Biochim Polym 2005, 52, 741.
30. Kmiecik, S.; Kurcinski, M.; Rutkowska, A.; Gront, D.; Kolinski, A. Acta Biochim Polym 2006, 53, 131.
31. De Sancho, D.; Prieto, L.; Rubio, A. M.; Rey, A. J Comput Chem 2005, 26, 131.
32. Goldberg, D. E. Genetic Algorithms in Search, Optimization & Machine Learning; Addison-Wesley: Reading, 1989.
33. Unger, R. Struct Bond 2004, 110, 153.
34. Dill, K. A. Biochemistry 1990, 29, 7133.
35. Myers, J. K.; Pace, C. N. Biophys J 1996, 71, 2033.
36. Fernández-Recio, J.; Romero, A. J Mol Biol 1999, 290, 319.
37. Baldwin, R. L. J Biol Chem 2003, 278, 17581.
38. Michalewicz, Z. Genetic Algorithms + Data Structures = Evolution Programs; Springer: Berlin, 1999.
39. Djurdjevic, D. P.; Bigg, M. J. J Comput Chem 2006, 27, 1177.
40. Onuchic, J. N.; Wolynes, P. G. Curr Opin Struct Biol 2004, 14, 70.
41. Maxwell, K. L.; Yee, A. A.; Booth, V.; Arrowsmith, C. H.; Gold, M.; Davidson, A. R. J Mol Biol 2001, 308, 9.
42. Orengo, C. A.; Michie, A. D.; Jones, S.; Jones, D. T.; Swindells, M. B.; Thornton, J. M. Structure 1997, 5, 1093.
43. Murzina, A. G.; Brennera, S. E.; Hubbarda, T.; Chothia, C. J Mol Biol 1995, 247, 536.
44. Humphrey, W.; Dalke, A.; Schulten, K. J Mol Graphics 1996, 14, 33.