Development and testing of PFFSol1.1, a new polarizable atomic force field for calculation of molecular interactions in implicit water environment

Journal of Physical Chemistry B

Volumn 116, Issue 15, 2012, Pages 4646-4654

  Pereyaslavets, Leonid B ^a   Finkelstein, Alexey V ^a  

^a INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; MOLECULES; OPTIMIZATION; PHASE TRANSITIONS; SOLVATION; SUBLIMATION; VACUUM; VAN DER WAALS FORCES;

ATOM-ATOM INTERACTION; ATOMIC FORCE FIELD; COVALENT INTERACTIONS; FORCE FIELDS; HENRY'S CONSTANTS; IN-VACUUM; NONBONDED INTERACTION; OPTIMIZED PARAMETER; PARTIAL CHARGES; PROTEIN INTERACTION; PROTEIN STRUCTURES; QUANTUM-MECHANICAL CALCULATION; ROOM TEMPERATURE; SOLVATION FREE ENERGIES; SOUGHT PARAMETERS; VAN DER WAALS; WATER ENVIRONMENTS; WATER MOLECULE;

CRYSTAL ATOMIC STRUCTURE;

EID: 84859984297     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp212474p     Document Type: Article

References (52)

1. Shaw, D. E.; Maragakis, P.; Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Eastwood, M. P.; Bank, J. A.; Jumper, J. M.; Salmon, J. K.; Shah, Y.; Wriggers, W. Science 2010, 330, 341
2. Lindorff-Larsen, K.; Piana, S.; Palmo, K.; Maragakis, P.; Klepeis, J. L.; Dror, R. O.; Shaw, D. E. Proteins 2010, 78, 1950
3. Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Shaw, D. E. Science 2011, 334, 517
4. Scheraga, H. A.; Leach, S. J.; Scott, R. A. Discuss. Faraday Soc. 1965, 40, 268
5. Scott, R. A.; Scheraga, H. A. J. Chem. Phys. 1965, 42, 2209
6. Edsall, J. T.; Flory, P. J.; Kendrew, J. C.; Liquori., A. M.; Nemethy, G.; Ramachandran, G. N.; Scheraga, H. A. J. Biol. Chem. 1966, 241, 1004
7. Leach, S. J.; Némethy, G.; Scheraga, H. A. Biopolymers 1966, 4, 369
8. Bixon, M.; Lifson, S. Tetrahedron 1967, 23, 769
9. Bixon, M.; Dekker, H.; Dunitz, J. D.; Eser, H.; Lifson, S.; Mosselman, C.; Sicher, J.; Svoboda, M. Chem. Commun. 1967, 360
10. Brant, D. A.; Miller, W.; Flory, P. J. J. Mol. Biol. 1967, 23, 47
11. Lifson, S.; Warshel, A. J. Chem. Phys. 1968, 49, 5116
12. Levitt, M.; Lifson, S. J. Mol. Biol. 1969, 46, 269
13. Kitaigorodsky, A. I. Molecular crystals; Nauka: Moscow, 1971, (in Russian; English translation: Kitaigorodsky, A. I. Molecular crystals and molecules; Academic Press: New York, 1973).
14. Hagler, A. T.; Huler, E.; Lifson, S. J. Am. Chem. Soc. 1974, 96, 5319
15. Brooks, B.; Bruccoleri, R.; Olafson, B.; States, D.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187
16. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; 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., III; 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
17. Levitt, M.; Hirshberg, M.; Sharon, R.; Daggett, V. Comput. Phys. Commun. 1995, 91, 215
18. Halgren, T. A. J. Comput. Chem. 1995, 17, 490
19. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. J. Comput. Chem. 2004, 25, 1157
20. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225
21. Donchev, A. G.; Ozrin, V. D.; Subbotin, M. V.; Tarasov, O. V.; Tarasov, V. I. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 7829
22. Kollman, P. A. Chem. Rev. 1993, 93, 2395
23. Khoruzhii, O. V.; Donchev, A. G.; Galkin, N. G.; Illarionov, A. A.; Olevanov, M. A.; Ozrin, V. D.; Queen, C.; Tarasov, V. I. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 10378
24. Roux, B.; Simonson, T. Biophys. Chem. 1999, 78, 1
25. Cramer, C. J.; Truhlar, D. G. Chem. Rev. 1999, 99, 2161
26. Ponder, J. W.; Case, D. A. Adv. Protein Chem. 2003, 66, 27
27. Halgren, T. A.; Damm, W. Curr. Opin. Struct. Biol. 2001, 11, 236
28. Wesson, L.; Eisenberg, D. Protein Sci. 1992, 1, 227
29. Gallicchio, E.; Zhang, L. Y.; Levy, R. M. J. Comput. Chem. 2002, 23, 517
30. Simonson, T. Rep. Prog. Phys. 2003, 66, 737
31. Baker, N. A. Curr. Opin. Struct. Biol. 2005, 15, 137
32. Wang, J.; Tan, C.; Tan, Y.-H.; Lu, Q.; Luo, R. Commun. Comput. Phys. 2008, 3, 1010
33. Ghosh, A.; Rapp, C. S.; Friesner, R. A. J. Phys. Chem. B. 1998, 102, 10983
34. Allen, F. H. Acta Crystallogr. 2002, B58, 380
35. Lide, D. R. CRC Handbook of Chemistry and Physics on CD; CRC Press: Boca Raton, FL, 2005.
36. Chickos, J. S.; Acree, W. E., Jr. J. Phys. Chem. Ref. Data 2002, 31, 537
37. Sander, R. http://www.mpch-mainz.mpg.de/sander/res/henry.html, 1999.
38. Bayly, C. I.; Cieplak, P.; Cornell, W.; Kollman, P. A. J. Phys. Chem. 1993, 97, 10269
39. Pereyaslavets, L. B.; Finkelstein, A. V. Mol. Biol. 2010, 44, 303
40. Finkelstein, A. V.; Pereyaslavets, L. B. Matematicheskaia Biol. Bioinf. 2010, 5, 138
41. Landau, L. D.; Lifshitz, E. M. Quantum mechanics: non-relativistic theory; Pergamon: New York, 1991; p 86.
42. Finkelstein, A. V.; Ptitsyn, O. B. Protein physics, 3 rd Russian ed.; problem 3.4; Knizhy dom Universitet: Moscow, 2005.
43. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127
44. Pohl, R. W. Eleketrizitätslehre; Springer-Verlag: Berlin, 1960; pp 115-116.
45. Finkelstein, A. V. Chem. Central J. 2007, 1, 21
46. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Kollman, P.A. J. Am. Chem. Soc. 1993, 115, 9620
47. Granovsky, A. A. http://classic.chem.msu.su/gran/gamess/index.html, 2008.
48. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery, J. A. J. Comput. Chem. 1993, 14, 1347
49. Wang, J.; Wang, W.; Kollman, P. A.; Case, D. A. J. Mol. Graph. Model. 2006, 25, 247-260
50. Pauling, L. General chemistry; W. H. Freeman & Co: New York, 1970; Chapters 6, 11.
51. Ewig, C. S.; Thacher, T. S.; Hagler, A. T. J. Phys. Chem. B 1999, 103, 6998
52. Donchev, A. G.; Galkin, N. G.; Illarionov, A. A.; Khoruzhii, O. V.; Olevanov, M. A.; Ozrin, V. D.; Pereyaslavets, L. B.; Tarasov, V. I. J. Comput. Chem. 2008, 29, 1242