-
2
-
-
35548967122
-
-
Molecular Simulation; Academic Press: San Diego, CA
-
Frenkel, D.; Smith, B. Understanding Molecular Simulation; Academic Press: San Diego, CA, 2001; Vol. 1.
-
(2001)
Understanding
, vol.1
-
-
Frenkel, D.1
Smith, B.2
-
5
-
-
0029011701
-
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
-
(1995)
J. Am. Chem. Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz Jr., K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
6
-
-
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.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586-3616.
-
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.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586-3616.
-
-
-
-
7
-
-
0029912748
-
-
Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236.
-
(1996)
J. Am. Chem. Soc
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
8
-
-
0035425883
-
-
Schuler, L. D.; Daura, X.; van Gunsteren, W. F. J. Comput. Chem. 2001, 22, 1205-1218.
-
(2001)
J. Comput. Chem
, vol.22
, pp. 1205-1218
-
-
Schuler, L.D.1
Daura, X.2
van Gunsteren, W.F.3
-
9
-
-
0026487174
-
-
Stickle, D. F.; Presta, L. G.; Dill, K. A.; Rose, G. D. J. Mol. Biol. 1992, 226, 1143-1159.
-
(1992)
J. Mol. Biol
, vol.226
, pp. 1143-1159
-
-
Stickle, D.F.1
Presta, L.G.2
Dill, K.A.3
Rose, G.D.4
-
10
-
-
0037434686
-
-
Ireta, J.; Neugebauer, J.; Scheffler, M.; Rojo, A.; Galván, M. J. Phys. Chem. B 2003, 107, 1432-1437.
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 1432-1437
-
-
Ireta, J.1
Neugebauer, J.2
Scheffler, M.3
Rojo, A.4
Galván, M.5
-
11
-
-
29044449043
-
-
Ireta, J.; Neugebauer, J.; Scheffler, M.; Rojo, A.; Galván, M. J. Am. Chem. Soc. 2005, 127, 17241-17244.
-
(2005)
J. Am. Chem. Soc
, vol.127
, pp. 17241-17244
-
-
Ireta, J.1
Neugebauer, J.2
Scheffler, M.3
Rojo, A.4
Galván, M.5
-
12
-
-
0034829669
-
-
Improta, R.; Barone, V.; Kudin, K.; Scuseria, G. E. J. Am. Chem. Soc. 2001, 123, 3311-3322.
-
(2001)
J. Am. Chem. Soc
, vol.123
, pp. 3311-3322
-
-
Improta, R.1
Barone, V.2
Kudin, K.3
Scuseria, G.E.4
-
15
-
-
84906389894
-
-
The DFT calculations of refs 11 and 14 employed ab initio pseudopotentials in conjunction with a plane-wave basis set of 70 Ry energy cutoff. The Perdew-Burke-Ernzerhof generalized gradient approximation was used to describe the electronic exchange and correlation interaction and the Brilloin-zone integration was replaced by the Γ-point. Greater details can be found in ref 11.
-
The DFT calculations of refs 11 and 14 employed ab initio pseudopotentials in conjunction with a plane-wave basis set of 70 Ry energy cutoff. The Perdew-Burke-Ernzerhof generalized gradient approximation was used to describe the electronic exchange and correlation interaction and the Brilloin-zone integration was replaced by the Γ-point. Greater details can be found in ref 11.
-
-
-
-
16
-
-
30344484542
-
-
Sorin, E. J.; Rhee, Y. M.; Shirts, M. R.; Pande, V. S. J. Mol. Biol. 2006, 356, 248-256.
-
(2006)
J. Mol. Biol
, vol.356
, pp. 248-256
-
-
Sorin, E.J.1
Rhee, Y.M.2
Shirts, M.R.3
Pande, V.S.4
-
17
-
-
41349102921
-
-
Ismer, L.; Ireta, J.; Boeck, S.; Neugebauer, J. Phys. Rev. E 2005, 71, 031911.
-
(2005)
Phys. Rev. E
, vol.71
, pp. 031911
-
-
Ismer, L.1
Ireta, J.2
Boeck, S.3
Neugebauer, J.4
-
18
-
-
45849102104
-
-
Ismer, L.; Ireta, J.; Neugebauer, J. J. Phys. Chem. B. 2008, 112, 4109-4112.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 4109-4112
-
-
Ismer, L.1
Ireta, J.2
Neugebauer, J.3
-
19
-
-
0037414279
-
-
Hartings, M. R.; Kinnear, B. S.; Jarrold, M. F. J. Am. Chem. Soc. 2003, 125, 3941-3947.
-
(2003)
J. Am. Chem. Soc
, vol.125
, pp. 3941-3947
-
-
Hartings, M.R.1
Kinnear, B.S.2
Jarrold, M.F.3
-
21
-
-
24144469823
-
-
Chin, W.; Piuzzi, F.; Dognon, J.-P.; Dimicoli, I.; Tardivel, B.; Mons, M. J. Am. Chem. Soc. 2005, 127, 11900-11901.
-
(2005)
J. Am. Chem. Soc
, vol.127
, pp. 11900-11901
-
-
Chin, W.1
Piuzzi, F.2
Dognon, J.-P.3
Dimicoli, I.4
Tardivel, B.5
Mons, M.6
-
22
-
-
33750623994
-
-
Abo-Riziq, A.; Bushnell, J. E.; Crews, B.; Callahan, M.; Grace, L.; de Vries, M. S. Chem. Phys. Lett. 2006, 431, 227-230.
-
(2006)
Chem. Phys. Lett
, vol.431
, pp. 227-230
-
-
Abo-Riziq, A.1
Bushnell, J.E.2
Crews, B.3
Callahan, M.4
Grace, L.5
de Vries, M.S.6
-
23
-
-
34249895893
-
-
Wei, Y.; Nadler, W.; Hansmann, U. H. E. J. Chem. Phys. 2007, 126, 204307.
-
(2007)
J. Chem. Phys
, vol.126
, pp. 204307
-
-
Wei, Y.1
Nadler, W.2
Hansmann, U.H.E.3
-
26
-
-
0035913529
-
-
Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. B 2001, 105, 6474-6487.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
28
-
-
33748518255
-
-
Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, A. R. C. Proteins 2006, 65, 712-725.
-
(2006)
Proteins
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, A.R.C.6
-
29
-
-
33947591301
-
-
Rasmussen, T. D.; Ren, P.; Ponder, J. W.; Jensen, F. Int. J. Quantum Chem. 2007, 107, 1390-1395.
-
(2007)
Int. J. Quantum Chem
, vol.107
, pp. 1390-1395
-
-
Rasmussen, T.D.1
Ren, P.2
Ponder, J.W.3
Jensen, F.4
-
31
-
-
33846595224
-
-
Jurečka, P.; Černý, J.; Hobza, P.; Salahub, D. S. J. Comput. Chem. 2007, 28, 555-569.
-
(2007)
J. Comput. Chem
, vol.28
, pp. 555-569
-
-
Jurečka, P.1
Černý, J.2
Hobza, P.3
Salahub, D.S.4
-
34
-
-
84906404405
-
-
6, terms, r being the interatomic distance. Note, however, that the range of r relevant to our discussion is large enough to make the repulsive term negligible.
-
6, terms, r being the interatomic distance. Note, however, that the range of r relevant to our discussion is large enough to make the repulsive term negligible.
-
-
-
-
35
-
-
2342593131
-
-
Morozov, A. V.; Kortemme, T.; Tsemekhman, K.; Baker. D. Proc. Natl. Acad. Sci. USA 2004, 101, 6946-6951.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 6946-6951
-
-
Morozov, A.V.1
Kortemme, T.2
Tsemekhman, K.3
Baker, D.4
-
37
-
-
33645519934
-
-
Morozov, A. V.; Tsemekhman, K.; Baker, D. J. Phys. Chem. B 2006, 110, 4503-4505.
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 4503-4505
-
-
Morozov, A.V.1
Tsemekhman, K.2
Baker, D.3
-
39
-
-
0038054912
-
Phys. Chem. B
-
J
-
Feig, M.; MacKerell, A. D., Jr.; Brooks, C. L., III J. Phys. Chem. B 2003, 107, 2831-2836.
-
(2003)
, vol.107
, pp. 2831-2836
-
-
Feig, M.1
MacKerell Jr., A.D.2
Brooks III, C.L.3
-
40
-
-
3142714765
-
Comput. Chem
-
J
-
MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., III J. Comput. Chem. 2004, 25, 1400-1415.
-
(2004)
, vol.25
, pp. 1400-1415
-
-
MacKerell Jr., A.D.1
Feig, M.2
Brooks III, C.L.3
-
41
-
-
84906375737
-
-
The energy grid correction map approach of ref 40 was used to modify CHARMM22 so that it can reproduce the gas-phase (φ, ψ)-PES of the Ala dipeptide calculated at the MP2 level of theory.
-
The energy grid correction map approach of ref 40 was used to modify CHARMM22 so that it can reproduce the gas-phase (φ, ψ)-PES of the Ala dipeptide calculated at the MP2 level of theory.
-
-
-
|