-
1
-
-
36849122972
-
High-temperature equation of state by a perturbation method. I. Nonpolar gases
-
Zwanzig R.W. High-temperature equation of state by a perturbation method. I. Nonpolar gases J.Chem.Phys. 22:420-1426, 1954.
-
(1954)
J.Chem.Phys.
, vol.22
, pp. 420-1426
-
-
Zwanzig, R.W.1
-
2
-
-
0028155689
-
A new method for predicting binding affinity in computer-aided drug design
-
Åqvist, J., Medina, C., Samuelsson, J.-E. A new method for predicting binding affinity in computer-aided drug design. Protein Eng. 7:385-391, 1994.
-
(1994)
Protein Eng.
, vol.7
, pp. 385-391
-
-
Åqvist, J.1
Medina, C.2
Samuelsson, J.-E.3
-
3
-
-
13344282748
-
An approach to rapid estimation of relative binding affinities of enzyme inhibitors : Application to peptidomimetic inhibitors of the human immunodeficiency virus type 1 protease
-
Viswanadhan, V.N., Reddy, M.R., Wlodawer, A., Varney M.D., Weinstein, J.N. An approach to rapid estimation of relative binding affinities of enzyme inhibitors : Application to peptidomimetic inhibitors of the human immunodeficiency virus type 1 protease. J. Med. Chem. 39:705-712, 1996.
-
(1996)
J. Med. Chem.
, vol.39
, pp. 705-712
-
-
Viswanadhan, V.N.1
Reddy, M.R.2
Wlodawer, A.3
Varney, M.D.4
Weinstein, J.N.5
-
4
-
-
0028066542
-
The Fourier-Green's function and the rapid evaluation of molecular potentials
-
Harrison, R.W., Kourinov, I.V., Andrews, L.C., The Fourier-Green's function and the rapid evaluation of molecular potentials. Protein Eng. 7:359-369, 1994.
-
(1994)
Protein Eng.
, vol.7
, pp. 359-369
-
-
Harrison, R.W.1
Kourinov, I.V.2
Andrews, L.C.3
-
5
-
-
0028519286
-
Prediction of new serine proteinase inhibitors
-
Kurinov, I.V., Harrison, R.W. Prediction of new serine proteinase inhibitors. Nat. Struc. Biol. 1:735-743, 1994.
-
(1994)
Nat. Struc. Biol.
, vol.1
, pp. 735-743
-
-
Kurinov, I.V.1
Harrison, R.W.2
-
6
-
-
0028844980
-
Calculation of relative binding free energies and configurational entropies: A structual and themodynamic analysis of the nature of non-polar binding of thorombin inhibitors based on hirudin
-
Wang, J., Szewczuk, Z., Yue, S.-Y., Tsuda, Y., Konishi, Y., Purisima, E.O. Calculation of relative binding free energies and configurational entropies: A structual and themodynamic analysis of the nature of non-polar binding of thorombin inhibitors based on hirudin. J. Mol. Biol. 253: 473-492, 1995.
-
(1995)
J. Mol. Biol.
, vol.253
, pp. 473-492
-
-
Wang, J.1
Szewczuk, Z.2
Yue, S.-Y.3
Tsuda, Y.4
Konishi, Y.5
Purisima, E.O.6
-
7
-
-
0029000922
-
Prediction of drug binding affinities by comparative binding energy analysis
-
Ortiz, A.R., Pisabarro, M.T., Gago, F., Wade, R.C., Prediction of drug binding affinities by comparative binding energy analysis. J. Med. Chem. 38:2681-2691, 1995.
-
(1995)
J. Med. Chem.
, vol.38
, pp. 2681-2691
-
-
Ortiz, A.R.1
Pisabarro, M.T.2
Gago, F.3
Wade, R.C.4
-
8
-
-
0029063951
-
A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site
-
Holloway, M.K., Wai, J.M., Halgren, T.A. et al. A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site. J. Med. Chem. 38:305-317, 1995.
-
(1995)
J. Med. Chem.
, vol.38
, pp. 305-317
-
-
Holloway, M.K.1
Wai, J.M.2
Halgren, T.A.3
-
9
-
-
0030255303
-
Scoring noncovalent protein-ligand interactions : A continuous differentiable function tuned to compute binding affinities
-
Jain, A.N., Scoring noncovalent protein-ligand interactions : A continuous differentiable function tuned to compute binding affinities. J.Comput. Aided Mol.Des. 10:427-440, 1996.
-
(1996)
J.Comput. Aided Mol.Des.
, vol.10
, pp. 427-440
-
-
Jain, A.N.1
-
10
-
-
0028881193
-
Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity
-
Verkhivker, G., Appelt, K., Freer, S.T., Villafranca, J.E., Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity Protein Eng. 8:677-691, 1995.
-
(1995)
Protein Eng.
, vol.8
, pp. 677-691
-
-
Verkhivker, G.1
Appelt, K.2
Freer, S.T.3
Villafranca, J.E.4
-
11
-
-
0029119320
-
A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design
-
Wallqvist, A., Jernigan, R.L., Covell, D.G. A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design Protein Sci. 4:1881-1903, 1995
-
(1995)
Protein Sci.
, vol.4
, pp. 1881-1903
-
-
Wallqvist, A.1
Jernigan, R.L.2
Covell, D.G.3
-
12
-
-
0000934205
-
SMoG: De novo design method based on simple, fast, and accurate free energy estimates. 1. Methodology and supporting evidence
-
DeWitte, R.S., Shakhnovich, E.I. SMoG: De novo design method based on simple, fast, and accurate free energy estimates. 1. Methodology and supporting evidence. J. Am. Chem. Soc. 118:11733-11744, 1996.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11733-11744
-
-
DeWitte, R.S.1
Shakhnovich, E.I.2
-
13
-
-
0024362070
-
On the attribution of binding energy in antigen-antibody complexes McPC603, D1.3, and HyHEL-5
-
Novotny, J., Bruccoleri, R.E., Saul, F.A. On the attribution of binding energy in antigen-antibody complexes McPC603, D1.3, and HyHEL-5. Biochemistry 28:4735-4749, 1989.
-
(1989)
Biochemistry
, vol.28
, pp. 4735-4749
-
-
Novotny, J.1
Bruccoleri, R.E.2
Saul, F.A.3
-
14
-
-
0031547977
-
Empirical free energy calculations : A blind test and further improvements to the method
-
Novotny, J., Bruccoleri, R.E., Davis, M., Sharp, K.A. Empirical free energy calculations : A blind test and further improvements to the method. J. Mol. Biol. 268:401-411, 1997.
-
(1997)
J. Mol. Biol.
, vol.268
, pp. 401-411
-
-
Novotny, J.1
Bruccoleri, R.E.2
Davis, M.3
Sharp, K.A.4
-
15
-
-
0025886180
-
Toward the semiquantitative estimation of binding constants. Guides for peptide-peptide binding in aqueous solution
-
Williams, D.H., Cox, J.P.L., Doig, A.J. et al. Toward the semiquantitative estimation of binding constants. Guides for peptide-peptide binding in aqueous solution. J. Am. Chem. Soc. 113:7020-7030, 1991.
-
(1991)
J. Am. Chem. Soc.
, vol.113
, pp. 7020-7030
-
-
Williams, D.H.1
Cox, J.P.L.2
Doig, A.J.3
-
16
-
-
0028454828
-
The development of a simple empirical scoring junction to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
-
Böhm, H.-J. The development of a simple empirical scoring junction to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J. Comput. Aided Mol. Des. 8:243-256, 1994.
-
(1994)
J. Comput. Aided Mol. Des.
, vol.8
, pp. 243-256
-
-
Böhm, H.-J.1
-
17
-
-
0029995624
-
VALIDATE : A new method for the receptor-based prediction of binding affinities of novel ligands
-
Head, R.D., Smythe, M.L., Oprea, T.I., Waller, C.L., Green, S.M., Marshall, G.R. VALIDATE : A new method for the receptor-based prediction of binding affinities of novel ligands. J. Am. Chem. Soc. 118:3959-3969, 1996.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 3959-3969
-
-
Head, R.D.1
Smythe, M.L.2
Oprea, T.I.3
Waller, C.L.4
Green, S.M.5
Marshall, G.R.6
-
18
-
-
0030157593
-
A structural and energetics analysis of the binding of a series of N-acetylneuraminic-acid-based inhibitors to influenza virus sialidase
-
Taylor, N.R., von Itzstein, M. A structural and energetics analysis of the binding of a series of N-acetylneuraminic-acid-based inhibitors to influenza virus sialidase. J.Comput. Aided Mol. Des. 10:233-246, 1996.
-
(1996)
J.Comput. Aided Mol. Des.
, vol.10
, pp. 233-246
-
-
Taylor, N.R.1
Von Itzstein, M.2
-
19
-
-
0028805201
-
A strategy for theoretical binding constant, Ki, calculations for neuraminidase aromatic inhibitors designed on the basis of the active site structure of influenza virus neuraminidase
-
Jedrzejas, M.J., Singh, S., Brouillette, W.J., Air, G.M., Luo, M. A strategy for theoretical binding constant, Ki, calculations for neuraminidase aromatic inhibitors designed on the basis of the active site structure of influenza virus neuraminidase. Proteins 23:264-277, 1995.
-
(1995)
Proteins
, vol.23
, pp. 264-277
-
-
Jedrzejas, M.J.1
Singh, S.2
Brouillette, W.J.3
Air, G.M.4
Luo, M.5
-
20
-
-
0030021877
-
Computational method for relative binding energies of enzyme-substrate complexes
-
Zhang, T., Koshland, D.E. Jr. Computational method for relative binding energies of enzyme-substrate complexes Protein Sci. 5:348-356, 1996.
-
(1996)
Protein Sci.
, vol.5
, pp. 348-356
-
-
Zhang, T.1
Koshland Jr., D.E.2
-
21
-
-
0027087369
-
Calculation of the free energy of association for protein complexes
-
Horton, N., Lewis, M. Calculation of the free energy of association for protein complexes. Protein Sci. 1:169-181, 1992.
-
(1992)
Protein Sci.
, vol.1
, pp. 169-181
-
-
Horton, N.1
Lewis, M.2
-
22
-
-
0025744588
-
Computational method for the design of enzymes with altered substrate specificity
-
Wilson, C., Mace, J.E., Agard, D.A. Computational method for the design of enzymes with altered substrate specificity J. Mol. Biol. 220:495-506, 1991.
-
(1991)
J. Mol. Biol.
, vol.220
, pp. 495-506
-
-
Wilson, C.1
Mace, J.E.2
Agard, D.A.3
-
23
-
-
0028102849
-
Effect of conformational flexibility and solvation on receptor-ligand binding free energies
-
Vajda, S., Weng, Z., Rosenfeld, R., DeLisi, C. Effect of conformational flexibility and solvation on receptor-ligand binding free energies. Biochemistry 33:13977-13988, 1994.
-
(1994)
Biochemistry
, vol.33
, pp. 13977-13988
-
-
Vajda, S.1
Weng, Z.2
Rosenfeld, R.3
DeLisi, C.4
-
24
-
-
0022964504
-
Focusing of electric fields in the active site of Cu-Zn superoxide dismutase : Effects of ionic strength and amino-acid modification
-
Klapper. I., Hagstrom, R.. Fine, R., Sharp, K., Honig, B. Focusing of electric fields in the active site of Cu-Zn superoxide dismutase : Effects of ionic strength and amino-acid modification. Proteins 1:47-59, 1986.
-
(1986)
Proteins
, vol.1
, pp. 47-59
-
-
Klapper, I.1
Hagstrom, R.2
Fine, R.3
Sharp, K.4
Honig, B.5
-
25
-
-
84962478456
-
A boundary element method for molecular electrostatics with electrolyte effects
-
Yoon, B.J., Lenhoff, A.M. A boundary element method for molecular electrostatics with electrolyte effects. J. Comput. Chem. 11:1080-1086, 1990.
-
(1990)
J. Comput. Chem.
, vol.11
, pp. 1080-1086
-
-
Yoon, B.J.1
Lenhoff, A.M.2
-
26
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still, W.C., Tempczyk, A., Hawley, R.C., Hendrickson, T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112:6127-6129, 1990.
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
27
-
-
84988053694
-
An all atom force field for simulations of proteins and nucleic acids
-
Weiner, S.J., Kollman, P.A., Nguyen, D.T., Case, D.A. An all atom force field for simulations of proteins and nucleic acids. J. Comput. Chem. 7:230-252, 1986.
-
(1986)
J. Comput. Chem.
, vol.7
, pp. 230-252
-
-
Weiner, S.J.1
Kollman, P.A.2
Nguyen, D.T.3
Case, D.A.4
-
28
-
-
0011930746
-
Theory of hydrophobic bonding. II. The correlation of hydrocarbon solubility in water with solvent cavity surface area
-
Hermann, R.B. Theory of hydrophobic bonding. II. The correlation of hydrocarbon solubility in water with solvent cavity surface area. J. Phys. Chem. 76:2754-2759, 1972.
-
(1972)
J. Phys. Chem.
, vol.76
, pp. 2754-2759
-
-
Hermann, R.B.1
-
29
-
-
11744256643
-
Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent
-
Tomasi, J., Persico, M. Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent. Chem. Rev. 94:2027-2094, 1994.
-
(1994)
Chem. Rev.
, vol.94
, pp. 2027-2094
-
-
Tomasi, J.1
Persico, M.2
-
30
-
-
0017429069
-
Areas, volumes, packing, and protein structure
-
Richards, F.M. Areas, volumes, packing, and protein structure. Ann. Rev. Biophys. Bioeng. 6:151-176, 1977.
-
(1977)
Ann. Rev. Biophys. Bioeng.
, vol.6
, pp. 151-176
-
-
Richards, F.M.1
-
31
-
-
33845374932
-
Ionization potentials and electron affinities in aqueous solution
-
Pearson, R.G. Ionization potentials and electron affinities in aqueous solution. J. Am. Chem. Soc. 108:6109-6114, 1986.
-
(1986)
J. Am. Chem. Soc.
, vol.108
, pp. 6109-6114
-
-
Pearson, R.G.1
-
32
-
-
0025390935
-
MOPAC : A semiempirical molecular orbital program
-
Stewart, J.J.P. MOPAC : A semiempirical molecular orbital program J. Comput. Aided Mol. Des 4:1-105, 1990.
-
(1990)
J. Comput. Aided Mol. Des.
, vol.4
, pp. 1-105
-
-
Stewart, J.J.P.1
-
33
-
-
0017411710
-
The protein data bank: A computer-based archival file for macromolecular structures
-
Bernstein, F.C., Koetzl, T.F., Williams, G.J.B. et al. The protein data bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
-
(1977)
J. Mol. Biol.
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzl, T.F.2
Williams, G.J.B.3
-
34
-
-
0023438480
-
A method for fast energy estimation and visualization of protein-ligand interaction
-
Tomioka, N., Itai, A., Iitaka, Y. A method for fast energy estimation and visualization of protein-ligand interaction J. Comput. Aided Mol. Des. 1:197-210, 1987.
-
(1987)
J. Comput. Aided Mol. Des.
, vol.1
, pp. 197-210
-
-
Tomioka, N.1
Itai, A.2
Iitaka, Y.3
-
35
-
-
0001010885
-
Representation of van der Waals (vdW) interactions in molecular mechanics force fields : Potential form, combination rules, and vdW parameters
-
Halgren, T.A. Representation of van der Waals (vdW) interactions in molecular mechanics force fields : Potential form, combination rules, and vdW parameters. J. Am. Chem. Soc. 114:7827-7843, 1992.
-
(1992)
J. Am. Chem. Soc.
, vol.114
, pp. 7827-7843
-
-
Halgren, T.A.1
-
37
-
-
0027214259
-
Three-dimensional structure of the tetragonal crystal form of egg-white avidin in its functional complex with biotin at 2.7 Å resolution
-
Pugliese, L., Coda, A., Malcovati, M., Bolognesi, M. Three-dimensional structure of the tetragonal crystal form of egg-white avidin in its functional complex with biotin at 2.7 Å resolution. J. Mol. Biol. 231:698-710, 1993.
-
(1993)
J. Mol. Biol.
, vol.231
, pp. 698-710
-
-
Pugliese, L.1
Coda, A.2
Malcovati, M.3
Bolognesi, M.4
-
38
-
-
0015505516
-
Dihydrofolate reductase. Purification and characterization of the enzyme from an amethopterin-resistant mutant of Escherichia coli
-
Poe, M., Greenfield, N.J., Hirshfield, J.M., Williams, M.N., Hoogsteen, K. Dihydrofolate reductase. Purification and characterization of the enzyme from an amethopterin-resistant mutant of Escherichia coli. Biochemistry 11:1023-1030, 1972.
-
(1972)
Biochemistry
, vol.11
, pp. 1023-1030
-
-
Poe, M.1
Greenfield, N.J.2
Hirshfield, J.M.3
Williams, M.N.4
Hoogsteen, K.5
-
39
-
-
0020441466
-
Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7Å resolution
-
Bolin, J.T., Filman, D.J., Matthews, D.A., Hamlin, R.C., Kraut, J. Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7Å resolution. J. Biol. Chem. 257:13650-13662, 1982.
-
(1982)
J. Biol. Chem.
, vol.257
, pp. 13650-13662
-
-
Bolin, J.T.1
Filman, D.J.2
Matthews, D.A.3
Hamlin, R.C.4
Kraut, J.5
-
40
-
-
0023835597
-
Quantitative structure-activity relationships for the inhibition of Escherichia coli dihydrofolate reductase by 5-(substituted benzyl)-2,4-diaminopyrimidines
-
Li, R.-L., Poe, M. Quantitative structure-activity relationships for the inhibition of Escherichia coli dihydrofolate reductase by 5-(substituted benzyl)-2,4-diaminopyrimidines. J. Med. Chem. 31:366-370, 1988.
-
(1988)
J. Med. Chem.
, vol.31
, pp. 366-370
-
-
Li, R.-L.1
Poe, M.2
-
41
-
-
0015384017
-
A second transport system for L-arabinose in Escherichia coli B/r controlled by the araC gene
-
Brown, C.E., Hogg, R.W. A second transport system for L-arabinose in Escherichia coli B/r controlled by the araC gene. J. Bacteriol. 111:606-613, 1972.
-
(1972)
J. Bacteriol.
, vol.111
, pp. 606-613
-
-
Brown, C.E.1
Hogg, R.W.2
-
42
-
-
0021205810
-
Novel stereospecificity of the L-arabinose-binding protein
-
Quiocho, F.A., Vyas, N.K. Novel stereospecificity of the L-arabinose-binding protein. Nature 310:381-386, 1984.
-
(1984)
Nature
, vol.310
, pp. 381-386
-
-
Quiocho, F.A.1
Vyas, N.K.2
-
43
-
-
0026454538
-
Protein-ligand energetics assessed using deoxy and fluorodeoxy sugars in equilibrium binding and high resolution crystallographic studies
-
Vermersch, P.S., Tesmer, J.J.G., Quiocho, F.A. Protein-ligand energetics assessed using deoxy and fluorodeoxy sugars in equilibrium binding and high resolution crystallographic studies. J.Mol.Biol. 226:923-929, 1992.
-
(1992)
J.Mol.Biol.
, vol.226
, pp. 923-929
-
-
Vermersch, P.S.1
Tesmer, J.J.G.2
Quiocho, F.A.3
-
44
-
-
0018801292
-
Location of the sugar-binding site of L-arabinose-binding protein
-
Newcomer, M.E., Miller, D.M., Quiocho, F.A. Location of the sugar-binding site of L-arabinose-binding protein. J. Biol. Chem. 254:7529-7533, 1979.
-
(1979)
J. Biol. Chem.
, vol.254
, pp. 7529-7533
-
-
Newcomer, M.E.1
Miller, D.M.2
Quiocho, F.A.3
-
46
-
-
0027985242
-
Rational automatic search method for stable docking models of protein and ligand
-
Mizutani, M., Tomioka, N., Itai, A. Rational automatic search method for stable docking models of protein and ligand. J. Mol. Biol. 243:310-326, 1994.
-
(1994)
J. Mol. Biol.
, vol.243
, pp. 310-326
-
-
Mizutani, M.1
Tomioka, N.2
Itai, A.3
-
47
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell, W.D., Cieplak, P., Bayly, C.I. et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179-5197, 1995.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
|