-
1
-
-
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
-
2
-
-
0004018984
-
Liquid state dynamics of alkane chains
-
Evans GT. Liquid state dynamics of alkane chains. ACS Adv Chem Ser 1983;204:423.
-
(1983)
ACS Adv Chem Ser
, vol.204
, pp. 423
-
-
Evans, G.T.1
-
3
-
-
0027080909
-
Atomic solvation parameters applied to molecular dynamics of proteins in solution
-
Wesson L, Eisenberg D. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci 1992;1:227-235.
-
(1992)
Protein Sci
, vol.1
, pp. 227-235
-
-
Wesson, L.1
Eisenberg, D.2
-
4
-
-
0015222647
-
The interaction of protein structures: Estimate of static accessibility
-
Lee B, Richards FM. The interaction of protein structures: Estimate of static accessibility. J Mol Biol 1971;55:379-400.
-
(1971)
J Mol Biol
, vol.55
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
-
5
-
-
0021755764
-
Solvent accessible surface area and excluded volume in proteins, analytical equations for overlapping spheres and implications for the hydrophobic effect
-
Richmond TJ. Solvent accessible surface area and excluded volume in proteins, analytical equations for overlapping spheres and implications for the hydrophobic effect. J Mol Biol 1984;178: 63-89.
-
(1984)
J Mol Biol
, vol.178
, pp. 63-89
-
-
Richmond, T.J.1
-
6
-
-
0000975320
-
Free energies of hydration of solute molecules. 4. Revised treatment of the hydration shell model
-
Kang YK, Gibson KD, Nemethy G, Scheraga HA. Free energies of hydration of solute molecules. 4. Revised treatment of the hydration shell model. J Phys Chem 1988;91:4739-4742.
-
(1988)
J Phys Chem
, vol.91
, pp. 4739-4742
-
-
Kang, Y.K.1
Gibson, K.D.2
Nemethy, G.3
Scheraga, H.A.4
-
7
-
-
0000280208
-
Exact calculation of the volume and surface area of fused hard-sphere molecules with unequal atomic radii
-
Gibson KD, Scheraga HA. Exact calculation of the volume and surface area of fused hard-sphere molecules with unequal atomic radii. Mol Phys 1987;62:1247-1265.
-
(1987)
Mol Phys
, vol.62
, pp. 1247-1265
-
-
Gibson, K.D.1
Scheraga, H.A.2
-
8
-
-
0001018540
-
Analytical approximation to the accessible surface area of proteins
-
Wodak SJ, Janin J. Analytical approximation to the accessible surface area of proteins. Proc Natl Acad Sci USA 1980;77:1736-1740.
-
(1980)
Proc Natl Acad Sci USA
, vol.77
, pp. 1736-1740
-
-
Wodak, S.J.1
Janin, J.2
-
9
-
-
0029155994
-
Hydrophobic potential by pairwise surface area sum
-
Kurochkina N, Lee B. Hydrophobic potential by pairwise surface area sum. Protein Eng 1995;8:437-442.
-
(1995)
Protein Eng
, vol.8
, pp. 437-442
-
-
Kurochkina, N.1
Lee, B.2
-
10
-
-
0007805550
-
A constraint dynamics algorithm for the simulation of semiflexible macromolecules
-
Wu XW, Sung SS. A constraint dynamics algorithm for the simulation of semiflexible macromolecules. J Comput Chem 1998; 19:1555-1566.
-
(1998)
J Comput Chem
, vol.19
, pp. 1555-1566
-
-
Wu, X.W.1
Sung, S.S.2
-
11
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J Comput Phys 1977;23: 327-341.
-
(1977)
J Comput Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
12
-
-
84952498828
-
On the force bias Monte Carlo simulation of water: Methodology, optimization, and comparison with molecular dynamics
-
Rao M, Pangali C, Berne BJ. On the force bias Monte Carlo simulation of water: Methodology, optimization, and comparison with molecular dynamics. Mol Phys 1979;37: 1773-1798.
-
(1979)
Mol Phys
, vol.37
, pp. 1773-1798
-
-
Rao, M.1
Pangali, C.2
Berne, B.J.3
-
13
-
-
0001456868
-
-
Lukos PG, editor. Washington, DC: American Chemical Society
-
Owicki JC. In: Lukos PG, editor. Computer modeling of matter. Washington, DC: American Chemical Society; 1978. p 159-171.
-
(1978)
Computer Modeling of Matter
, pp. 159-171
-
-
Owicki, J.C.1
-
14
-
-
0021757436
-
A new force field for molecular mechanical simulation of nucleic acids, and proteins
-
Weiner SJ, Kollman PA, Case DA, et al. A new force field for molecular mechanical simulation of nucleic acids, and proteins, J Am Chem Soc 1984;106:765-784.
-
(1984)
J Am Chem Soc
, vol.106
, pp. 765-784
-
-
Weiner, S.J.1
Kollman, P.A.2
Case, D.A.3
-
15
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandreskhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandreskhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
16
-
-
12044251376
-
A neutral, water-soluble, α-helical peptide: The effect of ionic strength on the helix-coil equilibrium
-
Scholtz JM, York EJ, Stewart JM, Baldwin RL. A neutral, water-soluble, α-helical peptide: The effect of ionic strength on the helix-coil equilibrium, J Am Chem Soc 1991;113: 5102-5104.
-
(1991)
J Am Chem Soc
, vol.113
, pp. 5102-5104
-
-
Scholtz, J.M.1
York, E.J.2
Stewart, J.M.3
Baldwin, R.L.4
-
17
-
-
0030006074
-
Molecular dynamics simulations of synthetic peptide folding
-
Sung SS, Wu XW. Molecular dynamics simulations of synthetic peptide folding. Proteins 1996;25: 202-214.
-
(1996)
Proteins
, vol.25
, pp. 202-214
-
-
Sung, S.S.1
Wu, X.W.2
-
18
-
-
0031282581
-
Molecular dynamics simulations of helix folding: The effects of amino acid substitution
-
Sung SS, Wu XW. Molecular dynamics simulations of helix folding: The effects of amino acid substitution. Biopolymers 1997; 42:633-644.
-
(1997)
Biopolymers
, vol.42
, pp. 633-644
-
-
Sung, S.S.1
Wu, X.W.2
-
19
-
-
0344557043
-
Molecular dynamics and Monte Carlo simulations favor the α-helical form for alanine-based peptides in water
-
Tirado-Rives J, Maxwell DS, Jorgensen WL. Molecular dynamics and Monte Carlo simulations favor the α-helical form for alanine-based peptides in water. J Am Chem Soc 1993;115:11590-11593.
-
(1993)
J Am Chem Soc
, vol.115
, pp. 11590-11593
-
-
Tirado-Rives, J.1
Maxwell, D.S.2
Jorgensen, W.L.3
-
20
-
-
0026525048
-
Molecular dynamics simulations of helix denaturation
-
Daggett, V., Levitt, M. Molecular dynamics simulations of helix denaturation. J. Mol. Biol. 223:1121-1138, 1992.
-
(1992)
J. Mol. Biol.
, vol.223
, pp. 1121-1138
-
-
Daggett, V.1
Levitt, M.2
-
21
-
-
0026748637
-
Differential helix propensity of small apolar side chains studied by molecular dynamics simulations
-
Hermans J, Anderson AG, Yun RH. Differential helix propensity of small apolar side chains studied by molecular dynamics simulations. Biochemistry 1992;31:5646-5653.
-
(1992)
Biochemistry
, vol.31
, pp. 5646-5653
-
-
Hermans, J.1
Anderson, A.G.2
Yun, R.H.3
-
22
-
-
0025767212
-
Thermodynamics and mechanism of α helix initiation in alanine and valine peptides
-
Tobias DJ, Brooks CL. III Thermodynamics and mechanism of α helix initiation in alanine and valine peptides. Biochemistry 1991;30:6059-6070.
-
(1991)
Biochemistry
, vol.30
, pp. 6059-6070
-
-
Tobias, D.J.1
Brooks C.L. III2
-
23
-
-
0029987862
-
Energy functions that discriminate X-ray and near-native folds from well-constructed decoys
-
Park B, Levitt M. Energy functions that discriminate X-ray and near-native folds from well-constructed decoys. J Mol Biol 1996; 258:367-392.
-
(1996)
J Mol Biol
, vol.258
, pp. 367-392
-
-
Park, B.1
Levitt, M.2
-
24
-
-
0004260243
-
-
New York: W.H. Freeman and Company
-
Creighton TE, editor. Protein folding. New York: W.H. Freeman and Company; 1992. p 1-547.
-
(1992)
Protein Folding
, pp. 1-547
-
-
Creighton, T.E.1
-
25
-
-
0030046906
-
Fast events in protein folding: Helix melting and formation in a small peptide
-
Williams S, Causgrove TP, Gilmanshin R, et al. Fast events in protein folding: Helix melting and formation in a small peptide. Biochemistry 1996;35:691-697.
-
(1996)
Biochemistry
, vol.35
, pp. 691-697
-
-
Williams, S.1
Causgrove, T.P.2
Gilmanshin, R.3
-
26
-
-
0030789351
-
Laser temperature jump study of the helix-coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model
-
Thompson PA, Eaton WA, Hofrichter J. Laser temperature jump study of the helix-coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model. Biochemistry 1997;36:9200-9210.
-
(1997)
Biochemistry
, vol.36
, pp. 9200-9210
-
-
Thompson, P.A.1
Eaton, W.A.2
Hofrichter, J.3
-
27
-
-
0344400158
-
Peptide folding simulations with explicit water-an equilibrium solvation method
-
Orlando, FL, August 25-29, p comp 0225
-
Wu XW, Sung SS. Peptide folding simulations with explicit water-an equilibrium solvation method. Book of abstract, 212th ACS National Meeting, American Chemical Society, Orlando, FL, August 25-29,1996. p comp 0225.
-
(1996)
Book of Abstract, 212th ACS National Meeting, American Chemical Society
-
-
Wu, X.W.1
Sung, S.S.2
|