-
1
-
-
33751385054
-
Macroscopic models of aqueous solutions: Biological and chemical applications
-
Honig, B., Sharp, K. and Yang, A. (1993). "Macroscopic models of aqueous solutions: biological and chemical applications", J. Phys. Chem., 97, 1101-1109.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 1101-1109
-
-
Honig, B.1
Sharp, K.2
Yang, A.3
-
2
-
-
0032968133
-
Implicit Solvent Models
-
Roux, B. and Simonson, T. (1999). "Implicit Solvent Models", Biophys. Chem., 78, 1-20.
-
(1999)
Biophys. Chem.
, vol.78
, pp. 1-20
-
-
Roux, B.1
Simonson, T.2
-
3
-
-
0024286089
-
Molecular dynamics simulations of ribonuclease T1: Analysis of the effect of solvent on the structure, fluctuations, and active site of the free enzyme
-
MacKerell, A. D. J., Nilsson, L., Rigler, R. and Saenger, W. (1988). "Molecular dynamics simulations of ribonuclease T1: analysis of the effect of solvent on the structure, fluctuations, and active site of the free enzyme", Biochemistry, 27, 4547-4556.
-
(1988)
Biochemistry
, vol.27
, pp. 4547-4556
-
-
MacKerell, A.D.J.1
Nilsson, L.2
Rigler, R.3
Saenger, W.4
-
4
-
-
0027080858
-
Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor
-
Guenot, J. and Kollman, P. A. (1992). "Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor", Prot. Sci., 1, 1185-205.
-
(1992)
Prot. Sci.
, vol.1
, pp. 1185-1205
-
-
Guenot, J.1
Kollman, P.A.2
-
5
-
-
0028146056
-
Molecular dynamics simulations of an enzyme surrounded by vacuum, water, or a hydrophobic solvent
-
Norm, M., Haeffner, F., Hult, K. and Edholm, O. (1994). "Molecular dynamics simulations of an enzyme surrounded by vacuum, water, or a hydrophobic solvent", Biophys. J., 67, 548-559.
-
(1994)
Biophys. J.
, vol.67
, pp. 548-559
-
-
Norm, M.1
Haeffner, F.2
Hult, K.3
Edholm, O.4
-
6
-
-
0344778061
-
Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics
-
Still, W. C., Tempczyk, A., Hawley, R. C. and Hendrickson, T. (1990). "Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics", J. Am. Chem. Soc., 112, 6127-6129.
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
7
-
-
34250928962
-
Volumes and Heats of Hydration of Ions
-
Born, M. (1920). "Volumes and Heats of Hydration of Ions", Z. Phys., 1, 45-48.
-
(1920)
Z. Phys.
, vol.1
, pp. 45-48
-
-
Born, M.1
-
8
-
-
0020475509
-
Calculation of the Electric Potential in the Active Site Cleft due to α-Helix Dipoles
-
Warwicker, J. and Watson, H. C. (1982). "Calculation of the Electric Potential in the Active Site Cleft due to α-Helix Dipoles", J. Mol. Bio., 157, 671-679.
-
(1982)
J. Mol. Bio.
, vol.157
, pp. 671-679
-
-
Warwicker, J.1
Watson, H.C.2
-
9
-
-
0023779259
-
Calculation of the Total Electrostatic Energy of a Macromolecular System: Solvation Energies, Binding Energies, and Conformational Analysis
-
Gilson, M. K. and Honig, B. (1988). "Calculation of the Total Electrostatic Energy of a Macromolecular System: Solvation Energies, Binding Energies, and Conformational Analysis", Proteins, 4, 7-18.
-
(1988)
Proteins
, vol.4
, pp. 7-18
-
-
Gilson, M.K.1
Honig, B.2
-
10
-
-
84986512474
-
CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations
-
Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. and Karplus, M. (1983). "CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations", J. Comp. Chem., 4, 187-217.
-
(1983)
J. Comp. 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
-
11
-
-
0031758128
-
Reduced protein models and their application to the protein folding problem
-
Skolnick, J., Kolinski, A. and Ortiz, A. R. (1998). "Reduced protein models and their application to the protein folding problem", J. Biomol. Struct. Dyn., 16, 381-396.
-
(1998)
J. Biomol. Struct. Dyn.
, vol.16
, pp. 381-396
-
-
Skolnick, J.1
Kolinski, A.2
Ortiz, A.R.3
-
12
-
-
0031059496
-
Theoretical studies of protein folding thermodynamics and kinetics
-
Shakhnovick, E. I. (1997). "Theoretical studies of protein folding thermodynamics and kinetics", Curr. Opin. Struct. Biol., 7, 29-40.
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 29-40
-
-
Shakhnovick, E.I.1
-
14
-
-
0026505184
-
Evaluation of Protein Models by Atomic Solvation Preference
-
Holm, L. and Sander, C. (1992). "Evaluation of Protein Models by Atomic Solvation Preference", J. Mol. Bio., 225, 93-105.
-
(1992)
J. Mol. Bio.
, vol.225
, pp. 93-105
-
-
Holm, L.1
Sander, C.2
-
16
-
-
4043171970
-
The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii
-
Qiu, D., Shenkin, P. S., Hollinger, F. P. and Still, W. C. (1997). "The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii", J. Phys. Chem. A, 101, 3005-3014.
-
(1997)
J. Phys. Chem. A
, vol.101
, pp. 3005-3014
-
-
Qiu, D.1
Shenkin, P.S.2
Hollinger, F.P.3
Still, W.C.4
-
17
-
-
0004161838
-
-
Press Syndicate of the University of Cambridge, New York
-
Press, W. H., Teukolsky, S. A., Vetterling, W. T. and Flannery, B. P., "Numerical Recipes in C", Press Syndicate of the University of Cambridge, New York, 1992.
-
(1992)
Numerical Recipes in C
-
-
Press, W.H.1
Teukolsky, S.A.2
Vetterling, W.T.3
Flannery, B.P.4
-
18
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
Honig, B. and Nicholls, A. (1995). "Classical electrostatics in biology and chemistry", Science, 268, 1144-1149.
-
(1995)
Science
, vol.268
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
19
-
-
6344260593
-
An All-Atom Empirical Energy Function for the Simulation of Nucleic Acids
-
MacKerell, A. D. Jr., Wiorkiewicz-Kuczera, J. and Karplus, M. (1995). "An All-Atom Empirical Energy Function for the Simulation of Nucleic Acids", J. Am. Chem. Soc., 117, 11946-11975.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 11946-11975
-
-
MacKerell A.D., Jr.1
Wiorkiewicz-Kuczera, J.2
Karplus, M.3
-
20
-
-
0041784950
-
All-atom Empirical Energy Function for Molecular Modeling and Dynamics Studies of Proteins
-
MacKerell, A. D. Jr., Bashford, D., Bellott, M., Dunbrack, R. L. Jr., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Gao, 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 III, W. E., Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D. and Karplus, M. (1998). "All-atom Empirical Energy Function for Molecular Modeling and Dynamics Studies of Proteins", J. Phys. Chem. B, 102, 3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell A.D., Jr.1
Bashford, D.2
Bellott, M.3
Dunbrack R.L., Jr.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Gao, 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 W.E. III20
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..
-
21
-
-
0000184330
-
Numerical integration of the Cartesian equations of motion for a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J. P., Ciccotti, G. and Berendsen, H. J. C. (1977). "Numerical integration of the Cartesian equations of motion for a system with constraints: molecular dynamics of n-alkanes", J. Comp. Phys., 52, 251-292.
-
(1977)
J. Comp. Phys.
, vol.52
, pp. 251-292
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
22
-
-
0032080053
-
Calculations on Folding of Segment B1 of Streptococcal Protein G
-
Sheinerman, F. B. and Brooks III, C. L. (1998). "Calculations on Folding of Segment B1 of Streptococcal Protein G", J. Mol. Bio., 278, 439-456.
-
(1998)
J. Mol. Bio.
, vol.278
, pp. 439-456
-
-
Sheinerman, F.B.1
Brooks C.L. III2
-
23
-
-
0030982583
-
A molecular dynamics simulation study of segment B1 of protein G
-
Sheinerman, F. B. and Brooks III, C. L. (1997). "A molecular dynamics simulation study of segment B1 of protein G", Proteins, 29, 193-202.
-
(1997)
Proteins
, vol.29
, pp. 193-202
-
-
Sheinerman, F.B.1
Brooks C.L. III2
-
24
-
-
0032539561
-
Molecular Picture of Folding of a Small Alpha/Beta Protein
-
Sheinerman, F. B. and Brooks III, C. L. (1998). "Molecular Picture of Folding of a Small Alpha/Beta Protein", PNAS, 95, 1562-1567.
-
(1998)
PNAS
, vol.95
, pp. 1562-1567
-
-
Sheinerman, F.B.1
Brooks C.L. III2
-
25
-
-
0017411710
-
The Protein Databank: A computer based archival file for macromolecular structures
-
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. and Tasumi, M. (1977). "The Protein Databank: A computer based archival file for macromolecular structures", J. Mol. Bio., 112, 535-542.
-
(1977)
J. Mol. Bio.
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
Meer, E.F.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
27
-
-
0033531959
-
Discrimination of the Native from Misfolded Protein Models with an Energy Function Including Implicit Solvation
-
Lazaridis, T. and Karplus, M. (1999). "Discrimination of the Native from Misfolded Protein Models with an Energy Function Including Implicit Solvation", J. Mol. Bio., 288, 477-487.
-
(1999)
J. Mol. Bio.
, vol.288
, pp. 477-487
-
-
Lazaridis, T.1
Karplus, M.2
-
28
-
-
32844457567
-
Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models
-
Sitkoff, D., Sharp, K. A. and Honig, B. (1994). "Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models", J. Am. Chem. Soc., 98, 1978-1988.
-
(1994)
J. Am. Chem. Soc.
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
29
-
-
0031075977
-
Solvation Free Energies of Peptides: Comparison of Approximate Continuum Solvation Models with Accurate Solution of the Poisson-Boltzmann Equation
-
Edinger, S. R., Cortis, C., Shenkin, P. S. and Friesner, R. A. (1997). "Solvation Free Energies of Peptides: Comparison of Approximate Continuum Solvation Models with Accurate Solution of the Poisson-Boltzmann Equation", J. Phys. Chem. B, 101, 1190-1197.
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 1190-1197
-
-
Edinger, S.R.1
Cortis, C.2
Shenkin, P.S.3
Friesner, R.A.4
-
30
-
-
0031872292
-
Discrimination between Native and Intentionally Misfolded Conformations of Proteins: ES/IS, a New Method for Calculating Conformational Free Energy That Uses Both Dynamics Simulations with an Explicit Solvent and an Implicit Solvent Continuum Model
-
Vorobjev, Y. N., Almagro, J. C. and Hermans, J. (1998). "Discrimination Between Native and Intentionally Misfolded Conformations of Proteins: ES/IS, a New Method for Calculating Conformational Free Energy That Uses Both Dynamics Simulations With an Explicit Solvent and an Implicit Solvent Continuum Model", Proteins, 32, 399-413.
-
(1998)
Proteins
, vol.32
, pp. 399-413
-
-
Vorobjev, Y.N.1
Almagro, J.C.2
Hermans, J.3
|