-
2
-
-
0002531265
-
Methods for calculation of free energies and binding constants: Successes and problems
-
Van Gunsteren, W. F., Weiner, P. K., Eds.; ESCOM Science Publishers, B. V.: Leiden, The Netherlands
-
van Gunsteren, W. F. Methods for calculation of free energies and binding constants: successes and problems. In Computer simulation of biomolecular systems: theoretical and experimental applications; Van Gunsteren, W. F., Weiner, P. K., Eds.; ESCOM Science Publishers, B. V.: Leiden, The Netherlands, 1989; pp 27-59.
-
(1989)
Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications
, pp. 27-59
-
-
Van Gunsteren, W.F.1
-
3
-
-
0001577491
-
Free energy perturbation calculations
-
Schleyer, P., Ed.; John Wiley and Sons: New York
-
Mark, A. E. Free energy perturbation calculations. In Encyclopaedia of computational chemistry; Schleyer, P., Ed.; John Wiley and Sons: New York, 1998; Vol. 2, pp 1070-1083.
-
(1998)
Encyclopaedia of Computational Chemistry
, vol.2
, pp. 1070-1083
-
-
Mark, A.E.1
-
6
-
-
36549092795
-
-
Jorgensen, W. L.; Buckner, I. K.; Boudon, S.; Tirado-Rives, J. J. Chem. Phys. 1988, 89, 3742-3746.
-
(1988)
J. Chem. Phys.
, vol.89
, pp. 3742-3746
-
-
Jorgensen, W.L.1
Buckner, I.K.2
Boudon, S.3
Tirado-Rives, J.4
-
7
-
-
0031058541
-
-
Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. Biophys, J. 1997, 72, 1047-1069.
-
(1997)
Biophys, J.
, vol.72
, pp. 1047-1069
-
-
Gilson, M.K.1
Given, J.A.2
Bush, B.L.3
McCammon, J.A.4
-
11
-
-
36449003554
-
-
Martyna, G. J.; Tobias, D. J.; Klein, M. L. J. Chem. Phys. 1994, 101, 4177-4189.
-
(1994)
J. Chem. Phys.
, vol.101
, pp. 4177-4189
-
-
Martyna, G.J.1
Tobias, D.J.2
Klein, M.L.3
-
12
-
-
36449007836
-
-
Feller, S. E.; Zhang, Y.; Pastor, R. W.; Brooks, B. R. J. Chem. Phys. 1995, 103, 4613-4621.
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 4613-4621
-
-
Feller, S.E.1
Zhang, Y.2
Pastor, R.W.3
Brooks, B.R.4
-
16
-
-
0030847766
-
-
Abola, E. E.; Sussman, J. L.; Prilusky, J.; Manning, N. O. Methods Enzymol. 1997, 277, 556-571.
-
(1997)
Methods Enzymol.
, vol.277
, pp. 556-571
-
-
Abola, E.E.1
Sussman, J.L.2
Prilusky, J.3
Manning, N.O.4
-
17
-
-
0032214622
-
-
Sussman, J. L.; Lin, D.; Jiang, J.; Manning, N. O.; Prilusky, J.; Ritter, O.; Abola, E. E. Acta Crystallogr. 1998, D54, 1078-1084.
-
(1998)
Acta Crystallogr.
, vol.D54
, pp. 1078-1084
-
-
Sussman, J.L.1
Lin, D.2
Jiang, J.3
Manning, N.O.4
Prilusky, J.5
Ritter, O.6
Abola, E.E.7
-
18
-
-
0024588901
-
-
Weber, P. C.; Ohlendorf, D. H.; Wendoloski, J. J.; Salemme, F. R. Science 1989, 243, 85-88.
-
(1989)
Science
, vol.243
, pp. 85-88
-
-
Weber, P.C.1
Ohlendorf, D.H.2
Wendoloski, J.J.3
Salemme, F.R.4
-
19
-
-
0026606240
-
-
Weber, P. C.; Wendoloski, J. J.; Pantoliano, M. W.; Salemme, F. R. J. Am. Chem. Soc. 1992, 114, 3197-3200.
-
(1992)
J. Am. Chem. Soc.
, vol.114
, pp. 3197-3200
-
-
Weber, P.C.1
Wendoloski, J.J.2
Pantoliano, M.W.3
Salemme, F.R.4
-
22
-
-
0030987036
-
-
Izrailev, S.; Stepaniants, S.; Baisera, M.; Oono, Y.; Schulten, K. Biophys. J. 1997, 72, 1568-1581.
-
(1997)
Biophys. J.
, vol.72
, pp. 1568-1581
-
-
Izrailev, S.1
Stepaniants, S.2
Baisera, M.3
Oono, Y.4
Schulten, K.5
-
30
-
-
0029170114
-
-
Cheatham III, T. E.; Miller, J. L.; Fox, T.; Darden, T. A.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 4193-4194.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 4193-4194
-
-
Cheatham III, T.E.1
Miller, J.L.2
Fox, T.3
Darden, T.A.4
Kollman, P.A.5
-
31
-
-
0030852818
-
-
Demchuk, E.; Bashford, D.; Case, D. A. J. Mol. Biol. 1997, 270, 305-317.
-
(1997)
J. Mol. Biol.
, vol.270
, pp. 305-317
-
-
Demchuk, E.1
Bashford, D.2
Case, D.A.3
-
32
-
-
0030862276
-
-
Young, M. A.; Ravishanker, G.; Beveridge, D. L. Biophys. J. 1997, 73, 2313-2336.
-
(1997)
Biophys. J.
, vol.73
, pp. 2313-2336
-
-
Young, M.A.1
Ravishanker, G.2
Beveridge, D.L.3
-
35
-
-
0032584783
-
-
Daura, X.; Jaun, B.; Seebach, D.; van Gunsteren, W. F.; Mark, A. E. J. Mol. Biol. 1998, 280, 925-932.
-
(1998)
J. Mol. Biol.
, vol.280
, pp. 925-932
-
-
Daura, X.1
Jaun, B.2
Seebach, D.3
Van Gunsteren, W.F.4
Mark, A.E.5
-
36
-
-
84986512474
-
-
Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
37
-
-
0004016501
-
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
38
-
-
0041784950
-
-
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, 3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher III, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
39
-
-
0042415783
-
-
Kale, L.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Gursoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadarajan, K.; Schulten, K. J. Comput. Phys. 1999, 151, 283-312. (Free energy calculation of an alchemical transformation is not a standard feature of NAMD2. Appropriate routines were written and incorporated by the authors and will be made available with future NAMD distributions.).
-
(1999)
J. Comput. Phys.
, vol.151
, pp. 283-312
-
-
Kale, L.1
Skeel, R.2
Bhandarkar, M.3
Brunner, R.4
Gursoy, A.5
Krawetz, N.6
Phillips, J.7
Shinozaki, A.8
Varadarajan, K.9
Schulten, K.10
-
45
-
-
33846823909
-
-
Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089-10092.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
46
-
-
33645961739
-
-
Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1995, 103, 8577-8593.
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
York, D.5
Pedersen, L.6
-
47
-
-
48749137581
-
-
Brünger, A.; Brooks, C. L., III; Karplus, M. Chem. Phys. Lett. 1984, 105, 495-500.
-
(1984)
Chem. Phys. Lett.
, vol.105
, pp. 495-500
-
-
Brünger, A.1
Brooks III, C.L.2
Karplus, M.3
-
48
-
-
0023346161
-
-
Bash, P. A.; Singh, U. C.; Langridge, R.; Kollman, P. A. Science 1987, 236, 564-568.
-
(1987)
Science
, vol.236
, pp. 564-568
-
-
Bash, P.A.1
Singh, U.C.2
Langridge, R.3
Kollman, P.A.4
-
52
-
-
0030601861
-
-
Brady, P.; Szabo, A.; Sharp, K. A. J. Mol. Biol. 1996, 253, 123-125.
-
(1996)
J. Mol. Biol.
, vol.253
, pp. 123-125
-
-
Brady, P.1
Szabo, A.2
Sharp, K.A.3
-
57
-
-
0000249851
-
-
Beutler, T. C.; Mark, A. E.; van Schaik, R. C.; Gerber, P. R.; van Gunsteren, W. F. Chem. Phys. Lett. 1994, 222, 529-539.
-
(1994)
Chem. Phys. Lett.
, vol.222
, pp. 529-539
-
-
Beutler, T.C.1
Mark, A.E.2
Van Schaik, R.C.3
Gerber, P.R.4
Van Gunsteren, W.F.5
|