AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules

Lifson, 1968, J. Chem. Phys., 49, 5116, 10.1063/1.1670007

Warshel, 1968, J. Chem. Phys., 53, 582, 10.1063/1.1674031

Gelin, 1976

Weiner, 1981, J. Comput. Chem, 2, 287, 10.1002/jcc.540020311

Langridge, 1981, Science, 211, 661, 10.1126/science.7455704

Dearing, 1980

Ferrin, 1985

Weiner, 1984, J. Amer. Chem. Soc., 106, 765, 10.1021/ja00315a051

Weiner, 1986, J. Comput. Chem., 7, 230, 10.1002/jcc.540070216

Singh, 1984, J. Comput. Chem., 5, 129, 10.1002/jcc.540050204

Weiner, 1981

Berendsen, 1984, J. Chem. Phys., 81, 3684, 10.1063/1.448118

Singh, 1985, 82, 755

Seibel, 1985, 82, 6537

Singh, 1984

Jorgensen, 1985, J. Chem. Phys., 83, 3050, 10.1063/1.449208

Bash, 1987, Science, 235, 574, 10.1126/science.3810157

Bash, 1987, Science, 236, 564, 10.1126/science.3576184

Singh, 1987, J. Amer. Chem. Soc., 109, 1607, 10.1021/ja00240a001

Howard, 1988, J. Amer. Chem. Soc., 110, 6984, 10.1021/ja00229a009

Singh, 1986, J. Comput. Chem., 7, 718, 10.1002/jcc.540070604

Singh, 1986

Seibel, 1989

Seibel, 1991

Spellmeyer, 1990

Pearlman, 1991

Pearlman, 1994

Schafmeister, 1992

Pearlman, 1994, Interface: An interface design system

Pavitt, 1984, J. Comput. Chem, 5, 441, 10.1002/jcc.540050504

Allinger, 1989, J. Amer. Chem Soc., 111, 8551, 10.1021/ja00205a001

Hwang, 1994, J. Amer. Chem. Soc., 116, 2525

Cornell, 1995, J. Amer. Chem. Soc., 117, 5199, 10.1021/ja00124a002

Sun, 1992, J. Comput. Chem., 13, 33, 10.1002/jcc.540130105

Sun, 1992, J. Chem. Phys., 97, 5108, 10.1063/1.463832

Stanton, 1993, J. Phys. Chem., 97, 11868, 10.1021/j100148a005

Appelquist, 1971, J. Amer, Chem. Soc., 94, 2952, 10.1021/ja00764a010

Applequist, 1973, J. Chem. Phys., 58, 4251, 10.1063/1.1678981

1977, Accts, Chem. Res., 10, 79, 10.1021/ar50111a002

Applequist, 1979, J. Chem. Phys., 70, 1240, 10.1063/1.437616

1979, J. Applequist, J. Chem. Phys., 71, 1983, 10.1063/1.438517

1979, J. Applequist, J. Chem. Phys., 71, 4324, 10.1063/1.438238

1979, J. Applequist, J. Chem. Phys., 71, 4332, 10.1063/1.438239

1981, Biopolymers, 20, 387, 10.1002/bip.1981.360200210

1981, Biopolymers, 20, 2311, 10.1002/bip.1981.360201103

1982, Biopolymers, 21, 779, 10.1002/bip.360210405

Caldwell, 1984, Biopolymers, 23, 1891, 10.1002/bip.360231006

Lybrand, 1985, J. Chem. Phys., 83, 2923, 10.1063/1.449246

Cieplak, 1987, J. Chem. Phys, 87, 6393, 10.1063/1.452428

Ahlström, 1988, Theoretical Studies of Protein Solutions

Engström, 1989, Mol. Phys., 68, 459

Sprik, 1988, J. Chem. Phys., 89, 7556, 10.1063/1.455722

Straatsma, 1990, Mol. Simul., 5, 181, 10.1080/08927029008022130

1990, Chem. Phys. Lett., 167, 252, 10.1016/0009-2614(90)85014-4

J.B. Applequist, private communication

Caldwell, 1990, J. Amer. Chem. Soc., 112, 9144, 10.1021/ja00181a017

Dang, 1991, J. Amer Chem. Soc., 113, 2482, 10.1021/ja00007a021

Jorgensen, 1988, J. Amer. Chem. Soc., 110, 1657, 10.1021/ja00214a001

Jorgensen, 1983, J. Chem. Phys., 79, 926, 10.1063/1.445869

Brooks, 1983, J. Comput. Chem., 4, 187, 10.1002/jcc.540040211

Fletcher, 1964, Computer J., 7, 149, 10.1093/comjnl/7.2.149

Schlick, 1987, J. Comput. Chem., 8, 1025, 10.1002/jcc.540080711

van Gunsteren, 1993, Vol. 2., 3

Ryckaert, 1977, J. Comput. Phys., 23, 327, 10.1016/0021-9991(77)90098-5

Miyamoto, 1992, J. Comput. Chem., 13, 952, 10.1002/jcc.540130805

van Schaik, 1992, J. Comp.-Aided Mol. Design, 6, 97, 10.1007/BF00129422

1993

Wüthrich, 1989, Science, 243, 45, 10.1126/science.2911719

Bonvin, 1993, Vol. 2, 407

Gippert, 1990, Biochem. Pharm., 40, 15, 10.1016/0006-2952(90)90172-H

Borgias, 1990, Prog. NMR Spect., 22, 83, 10.1016/0079-6565(90)80015-A

Case, 1993, 53

Brüschweiler, 1994, J Prog. NMR Spectr., 26, 27, 10.1016/0079-6565(94)80003-0

Case, 1994, Meth. Enzymol., 239, 392, 10.1016/S0076-6879(94)39015-0

Pearlman, 1994, J. Biomol. NMR, 4, 279

Braun, 1985, J. Mol. Biol, 186, 611, 10.1016/0022-2836(85)90134-2

Torda, 1989, Chem. Phys. Lett., 157, 289, 10.1016/0009-2614(89)87249-5

Torda, 1990, J. Mol. Biol., 214, 223, 10.1016/0022-2836(90)90157-H

Torda, 1993, J. Biomol. NMR, 3, 55, 10.1007/BF00242475

Pearlman, 1991, J. Mol. Biol., 20, 457, 10.1016/0022-2836(91)90024-Z

Pearlman, 1994, J. Biomol. NMR, 4, 1

Palmer, 1992, J. Amer. Chem. Soc., 114, 9050

Brüschweiler, 1994, Phys. Rev. Lett., 72, 940, 10.1103/PhysRevLett.72.940

Yip, 1991, 317

Ösapay, 1991, J. Amer. Chem. Soc., 113, 9436, 10.1021/ja00025a002

Ösapay, 1994, J. Biomol. NMR, 4, 215, 10.1007/BF00175249

Ösapay, 1994, J. Mol. Biol., 244, 183, 10.1006/jmbi.1994.1718

Beveridge, 1989, Annu. Rev. Biophys. Biophys., 18, 431, 10.1146/annurev.bb.18.060189.002243

Pearlman, 1989, J. Chem. Phys., 90, 2460, 10.1063/1.455988

Straatsma, 1991, J. Chem. Phys, 95, 1175, 10.1063/1.461148

Pearlman, 1994, J. Phys. Chem., 98, 1487, 10.1021/j100056a020

Straatsma, 1986, J. Chem. Phys., 85, 6720, 10.1063/1.451846

Pearlman, 1989, J. Chem. Phys., 91, 7831, 10.1063/1.457251

Straatsma, 1986, Mol. Phys., 57, 89, 10.1080/00268978600100071

Pearlman, 1994, J. Comput. Chem., 15, 105, 10.1002/jcc.540150112

Pearlman, 1991, J. Chem. Phys., 94, 4532, 10.1063/1.460608

Straatsma, 1992, Chem. Phys. Lett., 196, 297, 10.1016/0009-2614(92)85971-C

Pearlman, 1993, J. Chem. Phys., 98, 8946, 10.1063/1.464453

Yun-yu, 1993, Protein Engineering, 6, 289, 10.1093/protein/6.3.289

Gao, 1989, Science, 244, 1069, 10.1126/science.2727695

Miyamoto, 1993, Proteins: Struct. Funct. Genet., 16, 226, 10.1002/prot.340160303

Mark, 1994, J. Mol. Biol., 240, 167, 10.1006/jmbi.1994.1430

Pearlman, 1995, J. Mol. Biol., 248, 696, 10.1006/jmbi.1995.0252

Cieplak, 1994, J. Chem. Phys., 101, 627, 10.1063/1.468117

Gerber, 1993, J. Comp. Ass. Mol. Des., 7, 305, 10.1007/BF00125505

Fleischman, 1987, J. Chem. Phys., 87, 3029, 10.1063/1.453039

Yu, 1988, J. Chem. Phys., 89, 5115, 10.1063/1.455080

Tobias, 1988, J. Chem. Phys., 89, 5115, 10.1063/1.455654

Pearlman, 1991, J. Am. Chem. Soc., 113, 7167, 10.1021/ja00019a012

Allen, 1987

Swope, 1982, J. Chem. Phys., 76, 637, 10.1063/1.442716

Berendsen, 1984, J. Chem. Phys., 81, 3684, 10.1063/1.448118

Guenot, 1993, J. Comput. Chem., 14, 295, 10.1002/jcc.540140306

Ferguson, 1995, J. Comput. Chem.

Andersen, 1980, J. Chem. Phys., 72, 2384, 10.1063/1.439486

D.M. Ferguson, Isothermal-Isobaric Molecular Dynamics Simulations with Monte Carlo Volume Sampling, Comp. Phys. Lett, in press.

Bennett, 1976, J. Comput. Phys., 22, 245, 10.1016/0021-9991(76)90078-4

Ferguson, 1993, J. Chem. Phys., 99, 10086, 10.1063/1.465517

Burkert, 1982

Ferguson, 1994, J. Glob. Opt., 4, 209, 10.1007/BF01096723

Niketic, 1977

Case, 1994, J. Curr. Opin. Struct. Biol., 4, 285, 10.1016/S0959-440X(94)90321-2

Brüschweiler, 1994, J Phys. Rev. Lett., 72, 940, 10.1103/PhysRevLett.72.940

Cerjan, 1981, J. Chem. Phys., 75, 2800, 10.1063/1.442352

Simons, 1983, J. Phys. Chem., 87, 2745, 10.1021/j100238a013

Nguyen, 1985, J. Phys. Chem., 89, 4020, 10.1021/j100265a018

Lamm, 1986, J. Chem. Phys, 85, 7335, 10.1063/1.451373

Kottalam, 1990, Biopolymers, 29, 1409, 10.1002/bip.360291008

Karplus, 1981, Macromolecules, 14, 325, 10.1021/ma50003a019

Levy, 1984, Macromolecules, 17, 1370, 10.1021/ma00137a013

Kitao, 1991, J. Chem. Phys., 158, 447, 10.1016/0301-0104(91)87082-7

Teeter, 1990, J. Phys. Chem., 94, 8091, 10.1021/j100384a021

DeBolt, 1993, J. Comput. Chem., 14, 312, 10.1002/jcc.540140307

DeBolt, 1994, J. Comput. Chem., 15, 351, 10.1002/jcc.540150310

van Gunsteren, 1977, Mol. Phys., 34, 1311, 10.1080/00268977700102571

Ryckaert, 1977, J. Comput. Phys., 34, 327, 10.1016/0021-9991(77)90098-5

Ciccotti, 1982, Mol. Phys., 47, 1253, 10.1080/00268978200100942

1994

Vincent, 1994

A.L. Beguelin, J.J. Dongarra, G.A. Geist, W.C. Jiang, R.J. Manchek, B.K. Moore and V.S. Sunderam, PVM Version 3.3: Parallel Virtual Machine System University of Tennessee, Knoxville TN; Oak Ridge National Laboratory, Oak Ridge TN; and Emory University, Altanta, Georgia.

Kabsch, 1976, Acta Cryst. A, 32, 922, 10.1107/S0567739476001873

Kabsch, 1976, Acta Cryst. A, 34, 827, 10.1107/S0567739478001680

Batschelet, 1981

Cremer, 1975, J. Amer. Chem. Soc., 96, 1354, 10.1021/ja00839a011

Altona, 1972, J. Amer. Chem. Soc., 94, 8205, 10.1021/ja00778a043

York, 1994, 91, 8715