Protein structure prediction aided by geometrical and probabilistic constraints

Journal of Computational Chemistry

Volumn 28, Issue 12, 2007, Pages 1943-1952

  Porwal, Gaurav ^a   Jain, Swapnil ^a   Babu, S Dhilly ^a   Singh, Deepak ^a   Nanavati, Hemant ^a   Noronha, Santosh ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY BOMBAY   (India)

Author keywords

Distance restraints; Loop backbone probability distribution; Monte Carlo minimization; Protein structure prediction; Secondary structure packing

Indexed keywords

ALGORITHMS; COMBINATORIAL OPTIMIZATION; CONSTRAINT THEORY; MONTE CARLO METHODS; PROBLEM SOLVING; PROTEINS;

DISTANCE RESTRAINTS; LOOP BACKBONE PROBABILITY DISTRIBUTION; PROTEIN STRUCTURE PREDICTION; SECONDARY STRUCTURE PACKING;

PROBABILISTIC LOGICS;

ALGORITHM; ARTICLE; MONTE CARLO METHOD; PROBABILITY; PROTEIN CONFORMATION; THERMODYNAMICS;

ALGORITHMS; MONTE CARLO METHOD; PROBABILITY; PROTEIN CONFORMATION; THERMODYNAMICS;

EID: 34547326786     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20736     Document Type: Article

References (46)

1. Al-Lazikani, B.; Jung, J.; Xiang, Z.; Honig, B. Curr Opin Struct Biol 2001, 5, 51.
2. Bonneau, R.; Baker, D. Annu Rev Biophys Biomol Struct 2001, 30, 173.
3. Schonbrun, J.; Wedemeyer, W. J.; Baker, D. Curr Opin Struct Biol 2002, 12, 348.
4. Kretsinger, R. H.; Ison, R. E.; Hovmöller, S. Methods Enzymol 2004, 383, 1.
5. Hardin, C.; Pogorelov, T. V.; Schulten, Z. L. Curr Opin Struct Biol 2002, 12, 76.
6. Simons, K. T.; Kooperberg, C.; Huang, E.; Baker, D. J Mol Biol 1997, 268, 209.
7. Rohl, C. A.; Strauss, C. E. M.; Misura, K. M. S.; Baker, D. Methods Enzymol 2004, 383, 66.
8. Skolnick, J.; Zhang, Y.; Arakaki, A. K.; Kolinski, A.; Boniecki, M.; Szilagyi, A.; Kihara, D. Proteins Struct Funct Genet 2003, 53, 469.
9. Scheraga, H. A. Biophys Chem 1996, 59, 329.
10. Yue, K.; Dill, K. A. Protein Sci 1995, 5, 254.
11. Yue, K.; Dill, K. A. Protein Sci 2000, 9, 1935.
12. Simon, I.; Nemethy, G.; Scheraga, H. A. Macromolecules 1978, 11, 797.
13. Gibson, K. D.; Scheraga, H. A. J Comput Chem 1987, 8, 826.
14. Duan, Y.; Kollman, P. A. Science 1998, 282, 740.
15. Orengo, C. A.; Taylor, W. R. Methods Enzymol 1996, 266, 617.
16. Abagyan, R.; Totrov, M. J Mol Biol 1994, 235, 983.
17. Evans, J. S.; Mathiowetz, A. M.; Chan, S. I.; Goddard W.A., III. Protein Sci 1995, 4, 1203.
18. Ozkan, S. B.; Meirovitch, H. J Comput Chem 2004, 25, 565.
19. Wang, G.; Dunbrack, R. L., Jr. Bioinformatics 2003, 19, 1589.
20. Jones, D. T. J Mol Biol 1999, 292, 195.
21. Garneir, J.; Gibrat, J. F.; Robson, B. Methods Enzymol 1996, 266, 540.
22. Zhang, Y.; Kolinski, A.; Skolnick, J. Biophys J 2003, 85, 1145.
23. Word, J. M. Ph.D. Dissertation, Duke University, Durham, NC, 2000, 274 pp.
24. Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Comput Phys Commun 1995, 91, 43.
25. Hao, M. H.; Rackovsky, S.; Liwo, A.; Pincus, M. R.; Scheraga, H. A. Proc Natl Acad Sci USA 1992, 89, 6614.
26. Salemme, F. R.; Weatherford, D. W. J Mol Biol 1981, 146, 101.
27. Salemme, F. R.; Weatherford, D. W. J Mol Biol 1981, 146, 119.
28. Ruczinski, I.; Kooperberg, C.; Bonneau, R.; Baker, D. Proteins Struct Funct Genet 2002, 48, 85.
29. Rost, B.; Liu, J. L.; Przybylski, D.; Nair, R.; Wrzeszczynski, K. O.; Bigelow, H.; Ofran, Y. In Handbook of Chemoinformatics - From Data to Knowledge; Gasteiger, J.; Engel, T., Eds.; Wiley: Weinheim, Germany, 2003; pp. 1789-1811.
30. Hubbard, T. J. P. In Proceedings of the Twenty-Seventh Annual Hawaii International Conference on System Sciences, Maui, Hawaii, January 4-7, 1994, pp. 336-344.
31. Janin, J.; Chothia, C. J Mol Biol 1980, 143, 95.
32. Cohen, F. E.; Sternberg, J. E.; Taylor, W. R. J Mol Biol 1982, 156, 821.
33. Chothia, C.; Levitt, M.; Richardson, D. J Mol Biol 1981, 145, 215.
34. Chou, K. C.; Nemethy, G.; Rumsey, S.; Tuttle, R. W.; Scheraga, H. A. J Mol Biol 1985, 186, 591.
35. Chou, K. C.; Nemethy, G.; Scheraga, H. A. J Phys Chem 1983, 87, 2869.
36. Ponder, J. W.TINKER: Software Tools for Molecular Design, Version 4.2; Washington University School of Medicine: Saint Louis, MO, 2004.
37. Li, Z.; Scheraga, H. A. Proc Natl Acad Sci USA 1987, 84, 6611.
38. Li, Z.; Scheraga, H. A. J Mol Struct (Theochem) 1988, 179, 333.
39. Abagyan, R. A.; Argos, P. J Mol Biol 1992, 225, 519.
40. Nocedal, J. Math Comput 1980, 35, 773.
41. Neria, E.; Fischer, S.; Karplus, M. J Chem Phys 1996, 105, 1902.
42. Nilsson, L.; Karplus, M. J Comput Chem 1986, 7, 591.
43. Reiher W. E., III. Ph.D. Thesis, Department of Chemistry, Harvard University, Cambridge, MA, 1985.
44. Qiu, D.; Shenkin, P. S.; Hollinger, F. P.; Still, W. C. J Phys Chem 1997, 101, 3005.
45. Canutescu, A. A.; Shelenkov, A. A.; Dunbrack, R. L., Jr. Protein Sci 2003, 12, 2001.
46. Depristo, M. A; De Bakker, P. I. W.; Shetty, R. P.; Blundell, T. L. Protein Sci 2003, 12, 2032.