-
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 K.M. Jr.5
6
Ferguson, D.M.7
Spellmeyer, D.C.8
Fox, T.9
Caldwell, J.W.10
Kollman, P.A.11
-
6
-
-
0029248338
-
-
Storer, J. W.; Giesen, D. J.; Cramer, C. J.; Truhlar, D. G. J. Comput.-Aided Mol. Design 1995, 9, 87-110.
-
(1995)
J. Comput.-Aided Mol. Design
, vol.9
, pp. 87-110
-
-
Storer, J.W.1
Giesen, D.J.2
Cramer, C.J.3
Truhlar, D.G.4
-
12
-
-
24244438779
-
-
White, C. A.; Johnson, B. G.; Gill, P. M. W.; Head-Gordon, M. Chem. Phys. Lett. 1994, 230, 8-16.
-
(1994)
Chem. Phys. Lett.
, vol.230
, pp. 8-16
-
-
White, C.A.1
Johnson, B.G.2
Gill, P.M.W.3
Head-Gordon, M.4
-
13
-
-
0002934876
-
-
Strain, M. C.; Scuseria, G. E.; Frisch, M. J. Science (Wash.) 1996, 271, 51-53.
-
(1996)
Science (Wash.)
, vol.271
, pp. 51-53
-
-
Strain, M.C.1
Scuseria, G.E.2
Frisch, M.J.3
-
15
-
-
0013357779
-
-
Lee, T.-S.; York, D. M.; Yang, W. J. Chem. Phys. 1996, 105, 2744-2750.
-
(1996)
J. Chem. Phys.
, vol.105
, pp. 2744-2750
-
-
Lee, T.-S.1
York, D.M.2
Yang, W.3
-
16
-
-
0028306109
-
-
Schindelin, H.; Jiang, W.; Inouye, M.; Heinemann, U. Proc. Nat. Acad. Sci. 1994, 91, 5119.
-
(1994)
Proc. Nat. Acad. Sci.
, vol.91
, pp. 5119
-
-
Schindelin, H.1
Jiang, W.2
Inouye, M.3
Heinemann, U.4
-
17
-
-
0003525155
-
-
John Wiley and Sons: New York
-
Brooks, C. L., III; Karplus, M.; Pettitt, B. M. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics; John Wiley and Sons: New York, 1988; Vol. LXXI.
-
(1988)
Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics
, vol.71
-
-
Brooks C.L. III1
Karplus, M.2
Pettitt, B.M.3
-
19
-
-
0004016501
-
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.3
Impey, R.W.4
Klein, M.L.5
-
20
-
-
0041598337
-
-
University of California, San Francisco
-
Pearlman, D. A.; Case, D. A.; Caldwell, J. C.; Seibel, G. L.; Singh, U. C.; Weiner, P.; Kollman, P. A. ; University of California, San Francisco, 1991.
-
(1991)
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.C.3
Seibel, G.L.4
Singh, U.C.5
Weiner, P.6
Kollman, P.A.7
-
21
-
-
0042099251
-
-
note
-
The coordinates for CspA were obtained from the Protein Data Bank (pdb entry pdb1mjc.ent) and the protein was placed at the center of a pre-equilibrated box of TIP3P Monte Carlo equilibrated water molecules. The box was truncated so as to include a 14 Å. thick solvent layer from the protein surface. The AMBER all atom force field with parm94.dat parameter set was used to model the protein. A uniform dielectric constant of ε=1 was used. Molecular dynamics simulations in the NTP ensemble consisted of a initial 100 steps of energy minimization using the steepest descent algorithm, followed by 575 picoseconds of dynamics with a 1 femtosecond timestep, in which the initial 75 ps was considered the equilibration period and the remaining 500 ps was the production run. All through out the simulations, we used a 15 Å non-bonded cut -off radius and a 25 time step update frequency of the non bonded pairlist. Coordinates were saved every 5 ps for future analysis.
-
-
-
-
24
-
-
0043101175
-
-
note
-
The unit negative charge was neutralized by protonating a surface Histidine residue and not through the addition of a counterion.
-
-
-
-
26
-
-
84986492477
-
-
Besler, B. H.; Merz, K. M. J.; Kollman, P. A. J. Comput. Chem. 1990, 11, 431-439.
-
(1990)
J. Comput. Chem.
, vol.11
, pp. 431-439
-
-
Besler, B.H.1
Merz, K.M.J.2
Kollman, P.A.3
-
27
-
-
84893169025
-
-
Frisch, M. J.; Baldridge, K. K.; Boatz, J. A.; Elbert, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nyugen, K. A.; Su, S. J.; Windus, T. L.; Dupuis, M.; Montgomery, J. A. J. Comput. Chem. 1993, 14, 1347.
-
(1993)
J. Comput. Chem.
, vol.14
, pp. 1347
-
-
Frisch, M.J.1
Baldridge, K.K.2
Boatz, J.A.3
Elbert, J.A.4
Elbert, S.T.5
Gordon, M.S.6
Jensen, J.H.7
Koseki, S.8
Matsunaga, N.9
Nyugen, K.A.10
Su, S.J.11
Windus, T.L.12
Dupuis, M.13
Montgomery, J.A.14
-
29
-
-
0000042113
-
-
Dang, L. X.; Rice, J. E.; Caldwell, J.; Kollman, P. A. J. Am. Chem. Soc. 1991, 113, 2481.
-
(1991)
J. Am. Chem. Soc.
, vol.113
, pp. 2481
-
-
Dang, L.X.1
Rice, J.E.2
Caldwell, J.3
Kollman, P.A.4
-
31
-
-
0042600323
-
-
note
-
This is not always true. In some cases the amount of charge transferred between molecules 1 and 2 (see Figure 1) are equivalent yielding no net transfer of charge.
-
-
-
-
32
-
-
0004344770
-
-
The Benjamin/Cummings Publishing Company, Inc.: Menlo Park, California
-
Turro, N. J. Modern Molecular Photochemistry; The Benjamin/Cummings Publishing Company, Inc.: Menlo Park, California, 1978.
-
(1978)
Modern Molecular Photochemistry
-
-
Turro, N.J.1
-
34
-
-
17344372213
-
-
Stavrev, K. K.; Zerner, M. C.; Meyer, T. J. J. Am. Chem. Soc. 1995, 117, 8684-8685.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 8684-8685
-
-
Stavrev, K.K.1
Zerner, M.C.2
Meyer, T.J.3
-
37
-
-
0032535959
-
-
Koritsanszky, T.; Flaig, R.; Zobel, D.; Krane, H.-G.; Morgenroth, W.; Luger, P. Science (Wash.) 1998, 279, 356-358.
-
(1998)
Science (Wash.)
, vol.279
, pp. 356-358
-
-
Koritsanszky, T.1
Flaig, R.2
Zobel, D.3
Krane, H.-G.4
Morgenroth, W.5
Luger, P.6
|