-
1
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
-
Duan Y, Kollman PA. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 1998;282:740-744; Duan Y, Kollman PA. State of the art in studying protein folding and protein structure prediction using molecular dynamics methods. J Mol Graph Model 2001;19:146-149.
-
(1998)
Science
, vol.282
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
2
-
-
0035005947
-
State of the art in studying protein folding and protein structure prediction using molecular dynamics methods
-
Duan Y, Kollman PA. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 1998;282:740-744; Duan Y, Kollman PA. State of the art in studying protein folding and protein structure prediction using molecular dynamics methods. J Mol Graph Model 2001;19:146-149.
-
(2001)
J Mol Graph Model
, vol.19
, pp. 146-149
-
-
Duan, Y.1
Kollman, P.A.2
-
3
-
-
0031565730
-
Modeling protein docking using shape complementarity, electrostatics, and biochemical information
-
For some recent equilibrium binding studies on the protein docking problem, see, for example, Gabb HA, Jackson RM, Sternberg MJE. Modeling protein docking using shape complementarity, electrostatics, and biochemical information. J Mol Biol 1997;272:106-120; Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function. J Comput Chem 1998;19:1639-1662; and Camacho CJ, Gatchell DW, Kimura SR, Vajda S. Scoring docked conformations generated by rigid-body protein-protein docking. Proteins 2000;40:525-537.
-
(1997)
J Mol Biol
, vol.272
, pp. 106-120
-
-
Gabb, H.A.1
Jackson, R.M.2
Sternberg, M.J.E.3
-
4
-
-
11644261806
-
Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function
-
For some recent equilibrium binding studies on the protein docking problem, see, for example, Gabb HA, Jackson RM, Sternberg MJE. Modeling protein docking using shape complementarity, electrostatics, and biochemical information. J Mol Biol 1997;272:106-120; Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function. J Comput Chem 1998;19:1639-1662; and Camacho CJ, Gatchell DW, Kimura SR, Vajda S. Scoring docked conformations generated by rigid-body protein-protein docking. Proteins 2000;40:525-537.
-
(1998)
J Comput Chem
, vol.19
, pp. 1639-1662
-
-
Morris, G.M.1
Goodsell, D.S.2
Halliday, R.S.3
Huey, R.4
Hart, W.E.5
Belew, R.K.6
Olson, A.J.7
-
5
-
-
0034663658
-
Scoring docked conformations generated by rigid-body protein-protein docking
-
For some recent equilibrium binding studies on the protein docking problem, see, for example, Gabb HA, Jackson RM, Sternberg MJE. Modeling protein docking using shape complementarity, electrostatics, and biochemical information. J Mol Biol 1997;272:106-120; Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function. J Comput Chem 1998;19:1639-1662; and Camacho CJ, Gatchell DW, Kimura SR, Vajda S. Scoring docked conformations generated by rigid-body protein-protein docking. Proteins 2000;40:525-537.
-
(2000)
Proteins
, vol.40
, pp. 525-537
-
-
Camacho, C.J.1
Gatchell, D.W.2
Kimura, S.R.3
Vajda, S.4
-
6
-
-
0041324187
-
Fokker-Planck equation and the grand molecular friction tensor for coupled rotational and translational motions of structured Brownian particles near structured surfaces
-
Peters MH. Fokker-Planck equation and the grand molecular friction tensor for coupled rotational and translational motions of structured Brownian particles near structured surfaces. J Chem Phys 1999;110:528-538.
-
(1999)
J Chem Phys
, vol.110
, pp. 528-538
-
-
Peters, M.H.1
-
7
-
-
0033070796
-
Fokker-Planck equation, molecular friction, and molecular dynamics for Brownian particle transport near external solid surfaces
-
Peters MH. Fokker-Planck equation, molecular friction, and molecular dynamics for Brownian particle transport near external solid surfaces. J Stat Phys 1999;94:557-573.
-
(1999)
J Stat Phys
, vol.94
, pp. 557-573
-
-
Peters, M.H.1
-
8
-
-
0042328476
-
The smoluchowski equation for structured macromolecules near structured surfaces
-
Peters MH. The smoluchowski equation for structured macromolecules near structured surfaces. J Chem Phys 2000;112:5488-5498.
-
(2000)
J Chem Phys
, vol.112
, pp. 5488-5498
-
-
Peters, M.H.1
-
9
-
-
51149202535
-
Brownian motion of polyatomic molecules: The coupling of rotational and translational motions
-
Condiff DW, Dahler JS. Brownian motion of polyatomic molecules: the coupling of rotational and translational motions. J Chem Phys 1966;44:3988-4005.
-
(1966)
J Chem Phys
, vol.44
, pp. 3988-4005
-
-
Condiff, D.W.1
Dahler, J.S.2
-
10
-
-
33750652614
-
Brownian dynamics with hydrodynamic interactions
-
Ermak DL, McCammon JA. Brownian dynamics with hydrodynamic interactions. J Chem Phys 1978;69:1352-1360.
-
(1978)
J Chem Phys
, vol.69
, pp. 1352-1360
-
-
Ermak, D.L.1
McCammon, J.A.2
-
13
-
-
0008164376
-
Rotational and translational dynamics of flexible macromolecules
-
Peters MH, Ying R. Rotational and translational dynamics of flexible macromolecules. J Chem Phys 1993;98:6492-6503.
-
(1993)
J Chem Phys
, vol.98
, pp. 6492-6503
-
-
Peters, M.H.1
Ying, R.2
-
14
-
-
0033954256
-
The protein data bank
-
Berman HM, Westbrook J, Feng Z, Gililand G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gililand, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
15
-
-
0029633168
-
GROMACS: A message passing parallel molecular dynamics implementation
-
Berendsen HJC, van der Spoel D, van Drunen R. GROMACS: a message passing parallel molecular dynamics implementation. Comp Phys Comm 1995;91:43-56; Lindahl E, Hess B, van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Mod 2001;7:306-317.
-
(1995)
Comp Phys Comm
, vol.91
, pp. 43-56
-
-
Berendsen, H.J.C.1
Van der Spoel, D.2
Van Drunen, R.3
-
16
-
-
0035789518
-
GROMACS 3.0: A package for molecular simulation and trajectory analysis
-
Berendsen HJC, van der Spoel D, van Drunen R. GROMACS: a message passing parallel molecular dynamics implementation. Comp Phys Comm 1995;91:43-56; Lindahl E, Hess B, van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Mod 2001;7:306-317.
-
(2001)
J Mol Mod
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
Van der Spoel, D.3
-
17
-
-
0030059225
-
Ligand binding: Molecular mechanics calculation of the streptavidin-biotin rupture force
-
and the references cited therein
-
See Grubmuller H, Heymann B, Tavan P. Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. Science 1996;271:997-1000; and the references cited therein.
-
(1996)
Science
, vol.271
, pp. 997-1000
-
-
Grubmuller, H.1
Heymann, B.2
Tavan, P.3
-
18
-
-
0001251663
-
Molecular dynamics study of atomic motions in water
-
Toukau K, Rahman A. Molecular dynamics study of atomic motions in water. Phys Rev B 1985;31:2643-2648.
-
(1985)
Phys Rev B
, vol.31
, pp. 2643-2648
-
-
Toukau, K.1
Rahman, A.2
-
19
-
-
4544369164
-
A generalized reaction field method for molecular dynamics simulations
-
Tironi IG, Sperb R, Smith PE, van Gunsteren WW. A generalized reaction field method for molecular dynamics simulations. J Chem Phys 1995;102:5451-5459.
-
(1995)
J Chem Phys
, vol.102
, pp. 5451-5459
-
-
Tironi, I.G.1
Sperb, R.2
Smith, P.E.3
Van Gunsteren, W.W.4
-
23
-
-
0021197643
-
Generalized hydrodynamics
-
Alder BJ, Alley WE. Generalized hydrodynamics. Phys Today 1984;January:56-63.
-
(1984)
Phys Today
, vol.JANUARY
, pp. 56-63
-
-
Alder, B.J.1
Alley, W.E.2
-
24
-
-
0011544343
-
Creeping flow about a sphere
-
Schmitz R, Felderhof BU. Creeping flow about a sphere. Physica 1978;92A:423-437.
-
(1978)
Physica
, vol.92 A
, pp. 423-437
-
-
Schmitz, R.1
Felderhof, B.U.2
-
25
-
-
0001682586
-
-
In computing the off-diagonal elements of the grand friction tensor for an isolated protein or peptide, we have used the well-known, general symmetric properties of this tensor for an arbitrarily shaped, isolated particle. Specifically, in computing the autocorrelation values for the spherical insulin and D-peptide systems, the (i, j) components and (j, i) components (j, ≠ i) were averaged, leading to the exact symmetrical tensor values shown. See Brenner H. J Coll Interface Sci 1967;23:407; Happel J, Nijhof; Brenner H, Low Reynolds number hydrodynamics. Dordrecht, Netherlands 1983.
-
(1967)
J Coll Interface Sci
, vol.23
, pp. 407
-
-
Brenner, H.1
-
26
-
-
0003502177
-
-
Dordrecht, Netherlands
-
In computing the off-diagonal elements of the grand friction tensor for an isolated protein or peptide, we have used the well-known, general symmetric properties of this tensor for an arbitrarily shaped, isolated particle. Specifically, in computing the autocorrelation values for the spherical insulin and D-peptide systems, the (i, j) components and (j, i) components (j, ≠ i) were averaged, leading to the exact symmetrical tensor values shown. See Brenner H. J Coll Interface Sci 1967;23:407; Happel J, Nijhof; Brenner H, Low Reynolds number hydrodynamics. Dordrecht, Netherlands 1983.
-
(1983)
Low Reynolds Number Hydrodynamics
-
-
Happel, J.1
Nijhof2
Brenner, H.3
-
27
-
-
0001660435
-
Prokaryotes
-
Hoppert M, Mayer F. Prokaryotes. Am Sci 1999;87:518-525.
-
(1999)
Am Sci
, vol.87
, pp. 518-525
-
-
Hoppert, M.1
Mayer, F.2
-
28
-
-
0010922913
-
Solvent Stokes-Einstein violation in aqueous protein solutions
-
Lamanna R, Delmelle M, Cannistraro S. Solvent Stokes-Einstein violation in aqueous protein solutions. Phys Rev E 1994;49:5878-5880.
-
(1994)
Phys Rev E
, vol.49
, pp. 5878-5880
-
-
Lamanna, R.1
Delmelle, M.2
Cannistraro, S.3
-
29
-
-
0033214895
-
Inhibiting HIV-1 entry: Discovery of D-peptide inhibitors that target gp41 coiled coil pocket
-
Eckert D, Nalashkevich V, Hong L, Carr P, Kim P. Inhibiting HIV-1 entry: discovery of D-peptide inhibitors that target gp41 coiled coil pocket. Cell 1999;99:103-115.
-
(1999)
Cell
, vol.99
, pp. 103-115
-
-
Eckert, D.1
Nalashkevich, V.2
Hong, L.3
Carr, P.4
Kim, P.5
|