Protein-specific force field derived from the fragment molecular orbital method can improve protein-ligand binding interactions

Journal of Computational Chemistry

Volumn 34, Issue 14, 2013, Pages 1251-1257

  Chang, Le ^a,b   Ishikawa, Takeshi ^c,d   Kuwata, Kazuo ^b,c   Takada, Shoji ^a,b  

^a KYOTO UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c GIFU UNIVERSITY   (Japan)

^d TOHOKU UNIVERSITY   (Japan)

Author keywords

ab initio molecular orbitals; fragment molecular orbital; in silico screening; molecular mechanics; restrained electrostatic potential

Indexed keywords

AB INITIO MOLECULAR ORBITALS; ELECTROSTATIC POTENTIALS; FRAGMENT MOLECULAR ORBITAL; FRAGMENT MOLECULAR ORBITAL METHODS; IN-SILICO SCREENING; PROTEIN-LIGAND BINDING AFFINITIES; RATIONAL DRUG DESIGNS; SECONDARY STRUCTURES;

AMBER; BINDING ENERGY; ELECTROSTATICS; ENZYMES; LIGANDS; MOLECULAR MECHANICS; MOLECULAR ORBITALS; ORBITAL CALCULATIONS;

PROTEINS;

ARCHAEAL PROTEIN; LIGAND; LYSOZYME;

ANIMAL; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CHICKEN; COMPUTER SIMULATION; HALOBACTERIUM SALINARUM; METABOLISM; PROTEIN BINDING; STATIC ELECTRICITY; THERMODYNAMICS;

ANIMALS; ARCHAEAL PROTEINS; CHICKENS; COMPUTER SIMULATION; HALOBACTERIUM SALINARUM; LIGANDS; MODELS, MOLECULAR; MURAMIDASE; PROTEIN BINDING; STATIC ELECTRICITY; THERMODYNAMICS;

EID: 84876669734     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.23250     Document Type: Article

References (25)

1. D. B. Kitchen, H. Decornez, J. R. Furr, J. Bajorath, Nat. Rev. Drug Discov. 2004, 3, 935.
2. P. Ferrara, H. Gohlke, D. J. Price, G. Klebe, C. L. Brooks, III, J. Med., Chem. 2004, 47, 3032.
3. S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, Jr, P. Weiner, J. Am., Chem. Soc. 1984, 106, 765.
4. S. J. Weiner, P. A. Kollman, D. T. Nguyen, D. A. Case, J. Comput. Chem. 1986, 7, 230.
5. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, M. Karplus, J. Comput., Chem. 1983, 4, 187.
6. T. A. Halgren, W. Damm, Curr. Opin. Struct. Biol. 2001, 11, 236.
7. Y. Tong, Y. Mei, Y. L. Li, C. G. Ji, J. Z. H. Zhang, J. Am., Chem. Soc. 2010, 132, 5137.
8. Y. Mei, Y. L. Li, J. Zeng, J. Z. H. Zhang, J. Comput., Chem. 2012, 33, 1374.
9. C. G. Ji, J. Z. H. Zhang, J. Comput., Chem. 2012, 33, 1416.
10. Y. Xiang, L. Duan, J. Z. H. Zhang, J. Chem., Phys. 2011, 134, 205101.
11. C. G. Ji, Y. Mei, J. Z. H. Zhang, Biophys. J., 2008, 9 5, 1080.
12. Y. Okiyama, H. Watanabe, K. Fukuzawa, T. Nakano, Y. Mochizuki, T. Ishikawa, S. Tanaka, K. Ebina, Chem. Phys. Lett. 2007, 449, 329.
13. Y. Okiyama, H. Watanabe, K. Fukuzawa, T. Nakano, Y. Mochizuki, T. Ishikawa, K. Ebina, S. Tanaka, Chem. Phys. Lett. 2009, 467, 417.
14. K. Kitaura, E. Ikeo, T. Asada, T. Nakano, M. Uebayasi, Chem. Phys. Lett. 1999, 313, 701.
15. M. S. Cordon, D. G. Fedorov, S. R. Pruitt, L. V. Slipchenko, Chem. Rev. 2012, 112, 632.
16. M. W. Schmidt, K. K. Baldridge, J. A. Boatz, S. T. Elbert, M. S. Gordon, J. H. Jensen, S. Koseki, N. Matsunaga, K. A. Nguyen, S. J. Su, T. L. Windus, M. Dupuis, J. A. Montgomery, J. Comput., Chem. 1993, 14, 1347.
17. D. G. Fedorov, K. Kitaura, J. Chem., Phys. 2004, 120, 6832.
18. C. I. Bayly, P. Cieplak, W. D. Cornell, P. A. Kollman, J. Phys., Chem. 1993, 97, 10269.
19. F.- Y. Dupradeau, A. Pigache, T. Zaffran, C. Savineau, R. Lelong, N. Grivel, D. Lelong, W. Rosanski, P. Cieplak, Phys. Chem. Chem. Phys. 2010, 12, 7821.
20. D. A. Pearlman, D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham, III, S. DeBolt, D. Ferguson, G. Seibel, P. Kollman, Comput. Phys. Commun. 1995, 91, 1.
21. R. Luo, L. David, M. K. Gilson, J. Comput., Chem. 2002, 23, 1244.
22. T. Ishikawa, K. Kuwata, J. Chem., Theory Comput., 2010, 6, 538.
23. M. Grininger, K. Zeth, D. Oesterhelt, J. Mol., Biol. 2006, 357, 842.
24. M. Schindler, Y. Assaf, N. Sharon, D. M. Chipman, Biochemistry 1977, 16, 423.
25. K. Maenaka, M. Matsushima, H. Song, F. Sunada, K. Watanabe, I. Kumagai, J. Mol., Biol. 1995, 247, 281.