Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models

Accounts of Chemical Research - Tập 33 Số 12 - Trang 889-897 - 2000
Peter A. Kollman1, Irina Massova1, Carolina Reyes1, Bernd Kuhn1, Shuanghong Huo1, Lillian T. Chong1, Matthew Lee1, Tai‐Sung Lee1, Yong Duan1, Wei Wang1, Oreola Donini1, Piotr Cieplak1, Jaysharee Srinivasan1, David A. Case1, Thomas E. Cheatham1
1Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, The Scripps Research Institute, LaJolla, California 92037, and Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112

Tóm tắt

Từ khóa


Tài liệu tham khảo

Allen M. P., 1987, Computer Simulation of Liquids

McCammon J. A., 1977, Nature, 267, 590, 10.1038/267585a0

Levitt, 1983, M. Computer Simulation of DNA Double-helix Dynamics. Cold Spring Harbor Symp. Quant. Biol.

Postma J. P. M., 1982, Faraday Symp. Chem. Soc.

Tembe B. L., 1984, Comput. Chem., 8, 283

Jorgensen W. L., 1985, J. Chem. Phys., 83, 3054

Kollman P. A, 1993, Chem. Rev., 93, 2417, 10.1021/cr00023a004

Darden T., 1993, J. Chem. Phys., 98, 10092, 10.1063/1.464397

Cheatham T. E., 1996, J. Mol. Biol., 259, 444

Srinivasan J., 1998, J. Am. Chem. Soc., 120, 9409

Vorobjev Y. N., 1998, Funct. Genet.

Jayaram B., 1998, J. Am. Chem. Soc., 120, 10633, 10.1021/ja981307p

Sitkoff D., 1998, J. Phys. Chem., 98, 1983

Cheatham T. E., 1997, Proc. Natl. Acad. Sci. U.S.A., 94, 9630, 10.1073/pnas.94.18.9626

Cheatham T. E., 1998, J. Biomol. Struct. Des., 16, 280

Cieplak P., 1997, J. Am. Chem. Soc., 119, 6730, 10.1021/ja963909j

Cheatham T. E., 1997, J. Am. Chem. Soc., 119, 4825, 10.1021/ja963641w

Arnott S., 1966, Nature, 211, 232, 10.1038/211227a0

Simmerling C., 1998, J. Am. Chem. Soc., 120, 7155

Miller J., 1997, Biophys. J., 73, 2710, 10.1016/S0006-3495(97)78298-5

Srinivasan J., 1998, J. Biomol. Struct. Dyn., 16, 682, 10.1080/07391102.1998.10508279

Duan Y., 1998, Science, 282, 744, 10.1126/science.282.5389.740

Lee M., 2000, Proteins, 39, 316

Lee M., J. Am. Chem. Soc., submitted.

Simons K. T., 1999, Funct. Genet.

Cordes M. H. J., 1999, Science, 284, 327

Cornell W., 1995, J. Am. Chem. Soc., 117, 5197, 10.1021/ja00124a002

Kollman P. A., 1997, Computer Simulations of Biomolecular Systems:  Computer Simulations of Biomolecular Systems

Kuhn B., J. Med. Chem., in press.

Wang J., 1998, Proteins, 34, 81

Wang W., 1999, Proteins, 34, 402

Kuhn B., 2000, J. Am. Chem. Soc, 122, 3916

Chong L. T., 1999, Proc. Natl. Acad. Sci. U.S.A., 96, 14335, 10.1073/pnas.96.25.14330

Patten P. A., 1996, Science, 271, 1091, 10.1126/science.271.5252.1086

Donini O., J. Med. Chem., in press.

Bottger A., 1997, J. Mol. Biol., 269, 756, 10.1006/jmbi.1997.1078

Massova I., 1999, J. Am. Chem. Soc., 121, 8143, 10.1021/ja990935j

Radmer R. J., 1998, J. Comput.-Aided Mol. Des., 12, 227, 10.1023/A:1007905722422

Wang W., J. Mol. Biol., in press.

Reyes C., 1999, RNA, 5, 244

Avis J. M., 1996, J. Mol. Biol., 257, 341

Allain F. H. T., 1996, Nature, 380, 650

Grubser C. C., 1996, Biochemistry, 35, 2267

Dubridge C., 1994, Nature, 372, 438

Reyes C., 2000, J. Mol. Biol., 297, 1158, 10.1006/jmbi.2000.3629

Reyes C., 2000, J. Mol. Biol., 295, 6, 10.1006/jmbi.1999.3319

Beveridge D. L., 2000, Curr. Opin. Struct. Biol., 10, 196, 10.1016/S0959-440X(00)00076-2

Jayaram B., 1999, J. Comput. Phys., 151, 357, 10.1006/jcph.1998.6173

Vorobjev C. Y. N., 1999, Biophys. Chem., 78, 205

Lee T., 2000, J. Am. Chem. Soc., 122, 4393

Froloff N., 1997, Protein Sci., 6, 1301, 10.1002/pro.5560060617

Miyamoto S., 1993, Proc. Natl. Acad. Sci. U.S.A., 90, 8406, 10.1073/pnas.90.18.8402

Williams D. J., 1999, Biophys. J., 76, 3205

Tsui V., 2000, J. Am. Chem. Soc., 122, 2498, 10.1021/ja9939385

Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E.; Ross, W. S.; Simmerling, C.; Darden, T.; Merz, K. M.; Stanton, R. V.; Chen, A.; Vincent, J. J.; Crowley, M.; Tsui, V.; Radmer, R.; Duan, Y.; Pitera, J.; Massova, I.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P. A. Amber 6; University of California, San Francisco, 2000.

Zou X. Q., 1999, J. Am. Chem. Soc., 121, 8043