Structure prediction of loops with fixed and flexible stems

Journal of Physical Chemistry B

Volumn 116, Issue 23, 2012, Pages 6670-6682

  Subramani, A ^a   Floudas, C A ^a  

^a Princeton University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CLUSTERING ALGORITHMS; DIHEDRAL ANGLE; FORECASTING; PROTEIN FOLDING; REFINING; TRAVELING SALESMAN PROBLEM;

ALL-ATOM FORCE FIELD; BACKBONE STRUCTURES; DATA SETS; ENERGY MINIMIZATION; GEOMETRY PROBLEMS; LOOP REGIONS; LOOP STRUCTURE; NUMBER OF ITERATIONS; OPTIMIZATION ALGORITHMS; OPTIMIZED STRUCTURES; PROBLEM-BASED; PROTEIN DATA BANK; PROTEIN FOLDING PROBLEM; ROTAMERS; SECONDARY STRUCTURES; SIDE-CHAINS; STRUCTURE PREDICTION; TORSION ANGLE; TRAVELING SALESMAN;

GEOMETRY;

EID: 84862285785     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp2113957     Document Type: Article

References (57)

1. Gunasekaran, K.; Ramakrishnan, C.; Balaram, P. Protein Eng. 1997, 10, 1131-1141
2. Weigelt, C. A.; Rossi, K. A.; Nayeem, A.; Krystek, S. R. Protein loop flexibility around ligand binding sites: Implications for drug design. Proceedings of the 235th ACS National Meeting, New Orleans, LA, 2008.
3. Fiser, A.; Do, R. K. G.; Sali, A. Protein Sci. 2000, 9, 1753-1773
4. Floudas, C. A.; Fung, H. K.; McAllister, S. R.; Mönnigmann, M.; Rajgaria, R. Chem. Eng. Sc. 2006, 61, 966-988
5. Floudas, C. A. Biotechnol. Bioeng. 2007, 97, 207-213
6. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res. 2000, 28, 235-242
7. Xiang, Z. X.; Soto, C. S.; Honig, B. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 7432-7437
8. Cohen, B. I.; Presnell, S. R.; Cohen, F. E. Protein Sci. 1993, 2, 2134-2145
9. Jacobson, M. P.; Pincus, D. L.; Rapp, C. S.; Day, T. J. F.; Honig, B.; Shaw, D. E.; Friesner, R. A. Proteins 2004, 55, 351-367
10. Li, X.; Jacobson, M. P.; Friesner, R. A. Proteins 2004, 55, 368-382
11. DePristo, M. A.; Bakker, P. I. W.; Lovell, S. C.; Blundell, T. L. Proteins 2003, 51, 41-55
12. Rohl, C. A.; Strauss, C. E. M.; Chivian, D.; Baker, D. Proteins 2004, 55, 656-677
13. Mönnigmann, M.; Floudas, C. A. Proteins 2005, 61, 748-762
14. Sellers, B. D.; Zhu, K.; Zhao, S.; Friesner, R. A.; Jacobson, M. P. Proteins 2008, 72, 959-971
15. Li, Y.; Rata, I.; Jakobsson, E. J. Chem. Inf. Model. 2011, 50, 1753-1773
16. Choi, Y.; Deane, C. M. Proteins 2010, 78, 1431-1440
17. Deane, C. M.; Blundell, T. L. Protein Sci. 2001, 10, 599-612
18. Michalsky, E.; Goede, A.; Preissner, R. Protein Eng. 2003, 16, 979-985
19. Fernandez-Fuentes, N.; Olivia, B.; Fiser, A. Nucleic Acids Res. 2006, 34, 2085-2097
20. Lessel, U.; Schomburg, D. Proteins 1999, 37, 56-64
21. Soto, C. S.; Fasnacht, M.; Zhu, J.; Forrest, L.; Honig, B. Proteins 2008, 70, 834-843
22. Spassov, V. Z.; Flook, P. K.; Yan, L. Prot. Eng., Des. Sel. 2008, 21, 91-100
23. Tosatto, S. C. E.; Blindewald, E.; Hesser, J.; Manner, R. Protein Eng. 2002, 15, 279-286
24. Zhu, K.; Pincus, D. L.; Zhao, S.; Friesner, R. A. Proteins 2006, 65, 438-452
25. Zhao, S.; Zhu, K.; Li, J.; Friesner, R. A. Proteins 2011, 79, 2920-2935
26. Cornell, W.; 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. 1995, 117, 5179-5197
27. MacKerell, A. D. J. Phys. Chem. B 1998, 102, 3586-3616
28. Némethy, G.; Gibson, K. D.; Palmer, K. A.; Yoon, C. N.; Paterlini, G.; Zagari, A.; Rumsey, S.; Scheraga, H. A. J. Phys. Chem. 1992, 96, 6472-6484
29. Jones, D. T. Proteins Suppl. 1997, 1, 185-191
30. de Bakker, P. I. W.; DePristo, M. A.; Burke, D. F.; Blundell, T. L. Proteins 2003, 51, 21-40
31. Bruccoleri, R.; Karplus, M. Biopolymers 1990, 29, 1847-1862
32. Higo, J.; Collura, V.; Garnier, J. Biopolymers 1992, 32, 33-43
33. Spasskov, V. J.; Flook, P. K.; Yan, L. Protein Eng. 2008, 21, 91-100
34. Felts, A. K.; Gallicchio, E.; Chekmarev, D.; Paris, K. A.; Friesner, R. A.; Levy, R. M. J. Chem. Theory Comput. 2008, 4, 855-868
35. Zhu, K.; Shirts, M. R.; Friesner, R. A. J. Chem. Theory Comput. 2007, 3, 2108-2119
36. Crippen, G. M.; Havel, T. F. Distance Geometry and Molecular Conformation; Wiley: New York, 1988.
37. Moré, J. J.; Wu, Z. J. Global Optim. 1999, 15, 219-234
38. Güntert, P.; Wüthrich, K. J. Biomol. NMR 1991, 1, 447-456
39. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Clarendon Press: Oxford, 1987.
40. Güntert, P. Q. Rev. Biophys. 1998, 31, 145-237
41. Güntert, P.; Mumenthaler, C.; Wüthrich, K. J. Mol. Biol. 1997, 273, 283-298
42. McAllister, S. R.; Floudas, C. A. Comput. Optim. Appl. 2010, 45, 377-413
43. Xiang, Z.; Honig, B. J. Mol. Biol. 2001, 311, 421-430
44. Desmet, J.; Spriet, J.; Lasters, I. Proteins 2002, 48, 31-43
45. Dunbrack, R. L. Curr. Opin. Struct. Biol. 2002, 12, 431-440
46. Gill, P. E.; Murray, W.; Saunders, M.; Wright, M. H. NPSOL 4.0 User's Guide; Systems Optimization Laboratory, Department of Operations Research, Stanford University: Stanford, CA, 1986.
47. Subramani, A.; DiMaggio, P. A.; Floudas, C. A. Biophys. J. 2009, 97, 1728-1736
48. DiMaggio, P. A.; Subramani, A.; Judson, R. S.; Floudas, C. A. Toxicol. Sci. 2010, 118, 251-265
49. DiMaggio, P. A.; McAllister, S. R.; Floudas, C. A.; Fend, X.-J.; Rabinowitz, J. D.; Rabitz, H. A. BMC Bioinformatics 2008, 97, 207-213
50. Applegate, D.; Bixby, R.; Chvatal, V.; Cook, W. The Traveling Salesman Problem: A Computational Study; Princeton University Press: Princeton, NJ, 2007.
51. Rajgaria, R.; McAllister, S. R.; Floudas, C. A. Proteins 2006, 65, 726-741
52. Rajgaria, R.; McAllister, S. R.; Floudas, C. A. Proteins 2007, 70, 950-970
53. Subramani, A.; Wei, Y.; Floudas, C. A. AIChE J. 2012, in press.
54. Ramachandran, G. N.; Ramakrishnan, C.; Sasisekharan, V. J. Mol. Biol. 1963, 7, 95-99
55. Wei, Y.; Thompson, J.; Floudas, C. A. Submitted for publication, 2011.
56. Ginalski, K.; Elofsson, A.; Fischer, D.; Rychlewski, L. Bioinformatics 2003, 19, 1015-1018
57. Altschul, S. F.; Madden, T. L.; Schäffer, A. A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D. J. Nucleic Acids Res. 1997, 25, 3389-3402