-
1
-
-
7044239742
-
Free energy calculation: Applications to chemical and biochemical phenomena
-
Kollman, P., Free energy calculation: Applications to chemical and biochemical phenomena, Chem. Rev., 93 (1993) 2395-2417.
-
(1993)
Chem. Rev.
, vol.93
, pp. 2395-2417
-
-
Kollman, P.1
-
2
-
-
0028237444
-
3-dimensional quantitavie structure-activity relationship of human- immunodeficiency-virus-(I) protease inhibitors: 2. Predictive power using limited exploration of alternate binding modes
-
Oprea, T.I., Waller, C.L. and Marshall, G.R., 3-dimensional quantitavie structure-activity relationship of human-immunodeficiency-virus-(I) protease inhibitors: 2. Predictive power using limited exploration of alternate binding modes,. J. Med. Chem., 37 (1994) 2206-2215.
-
(1994)
J. Med. Chem.
, vol.37
, pp. 2206-2215
-
-
Oprea, T.I.1
Waller, C.L.2
Marshall, G.R.3
-
3
-
-
0027762073
-
3- dimensional QSAR of human-immunodeficiency-virus-(I) protease inhibitors: 1. A COMFA study employing experimentally-determined alignment rules
-
Waller, C.L., Oprea, T.I., Giolitti, A. and Marshall, G.R., 3-dimensional QSAR of human-immunodeficiency-virus-(I) protease inhibitors: 1. A COMFA study employing experimentally-determined alignment rules, J. Med. Chem., 36 (1993) 4152-4160.
-
(1993)
J. Med. Chem.
, vol.36
, pp. 4152-4160
-
-
Waller, C.L.1
Oprea, T.I.2
Giolitti, A.3
Marshall, G.R.4
-
4
-
-
0028362672
-
Three-dimensional pharmacophores from binding data
-
Doweyko, A.M., Three-dimensional pharmacophores from binding data, J. Med. Chem., 37 (1994) 1769-1778.
-
(1994)
J. Med. Chem.
, vol.37
, pp. 1769-1778
-
-
Doweyko, A.M.1
-
5
-
-
0028455325
-
Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities
-
Meng, E.C., Kuntz, I.D., Abraham, D.J. and Kellogg, O.E., Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities, J. Comput.-Aided Mol. Design, 8 (1994) 299-306.
-
(1994)
J. Comput.-Aided Mol. Design
, vol.8
, pp. 299-306
-
-
Meng, E.C.1
Kuntz, I.D.2
Abraham, D.J.3
Kellogg, O.E.4
-
6
-
-
0029020486
-
Solvent accessibility as a predictive tool for the free-energy of inhibitor binding to the HlV-1 protease
-
Nauchitel, V., Villaverde, M.C. and Sussman, F., Solvent accessibility as a predictive tool for the free-energy of inhibitor binding to the HlV-1 protease, Protein Science, 4 (1995) 1356-1364.
-
(1995)
Protein Science
, vol.4
, pp. 1356-1364
-
-
Nauchitel, V.1
Villaverde, M.C.2
Sussman, F.3
-
7
-
-
0029989480
-
A possible involvement of solvent-induced interactions in drug design
-
Wang, H. and Ben-Naim, A., A possible involvement of solvent-induced interactions in drug design, J. Med. Chem., 39 (1996) 1531-1539.
-
(1996)
J. Med. Chem.
, vol.39
, pp. 1531-1539
-
-
Wang, H.1
Ben-Naim, A.2
-
8
-
-
0029119320
-
A preference-based free-energy parameterization of enzyme-inhibitor binding: Applications to HlV-1 protease inhibitor design
-
Wallqvist, A., Jernigan, R.L. and Covell, D.G., A preference-based free-energy parameterization of enzyme-inhibitor binding: Applications to HlV-1 protease inhibitor design, Protein Science, 4 (1995) 1881-1903.
-
(1995)
Protein Science
, vol.4
, pp. 1881-1903
-
-
Wallqvist, A.1
Jernigan, R.L.2
Covell, D.G.3
-
9
-
-
0029798563
-
Docking enzyme-inhibitor complexes using a preference-based free-energy surface
-
Wallqvist, A. and Covell, D.G., Docking enzyme-inhibitor complexes using a preference-based free-energy surface, Proteins: Struct., Funct. Gene., 25 (1996) 403-419.
-
(1996)
Proteins: Struct., Funct. Gene.
, vol.25
, pp. 403-419
-
-
Wallqvist, A.1
Covell, D.G.2
-
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., and 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 (1995) 677-691.
-
(1995)
Protein Eng.
, vol.8
, pp. 677-691
-
-
Verkhivker, G.1
Appelt, K.2
Freer, S.T.3
Villafranca, J.E.4
-
11
-
-
0030058373
-
A mean field model of ligand- protein interactions: Implications for the structural assessment of human immunodeficiency virus type I protease complexes and receptor-specific binding
-
Verkhivker, G.M. and Rejto, P.A., A mean field model of ligand-protein interactions: Implications for the structural assessment of human immunodeficiency virus type I protease complexes and receptor-specific binding, Proc. Natl. Acad. Sci. USA, 93 (1996) 60-64.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 60-64
-
-
Verkhivker, G.M.1
Rejto, P.A.2
-
12
-
-
84986432941
-
Automated docking with grid-based energy evaluation
-
Meng, E.G. Shoichet, B.K. and Kuntz, I.D., Automated docking with grid-based energy evaluation, J Comput. Chem., 13 (1992) 505.
-
(1992)
J Comput. Chem.
, vol.13
, pp. 505
-
-
Meng, E.G.1
Shoichet, B.K.2
Kuntz, I.D.3
-
13
-
-
0026848170
-
In search of new lead compounds for trypanosomiasis drug design: A protein structure-based linked-fragment approach
-
Verlinde, C.L.M.J., Rudenko, G., and Wim, G.J.H., In search of new lead compounds for trypanosomiasis drug design: a protein structure-based linked-fragment approach, J., Comput.-Aided Mol. Design, 6 (1992) 131-147.
-
(1992)
J., Comput.-Aided Mol. Design
, vol.6
, pp. 131-147
-
-
Verlinde, C.L.M.J.1
Rudenko, G.2
Wim, G.J.H.3
-
14
-
-
0027193713
-
Groupbuild: A fragment-based method for de novo drug design
-
Rotstein, S.H. and Murcko, M. A., Groupbuild: A fragment-based method for de novo drug design, J. Med. Chem., 36 (1993) 1700-1710.
-
(1993)
J. Med. Chem.
, vol.36
, pp. 1700-1710
-
-
Rotstein, S.H.1
Murcko, M.A.2
-
15
-
-
0028454828
-
The development of a simple empirical scoring function 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 function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure, J. Comput.-Aided Mol. Design, 8 (1994) 243-256.
-
(1994)
J. Comput.-Aided Mol. Design
, vol.8
, pp. 243-256
-
-
Böhm, H.-J.1
-
16
-
-
1542496902
-
De novo design of highly diverse structures complementary to enzyme binding sites: Application to thermolysin
-
Reynolds, C.H., Holloway, M.K. and Cox, H.K., (Eds.) Computer-aided molecular design: Applications in agrochemicals, materials and pharmaceuticals, American Chemical Society, Washington, DC
-
Bohacek, R.S.; McMartin, C., De novo design of highly diverse structures complementary to enzyme binding sites: Application to thermolysin, In Reynolds, C.H., Holloway, M.K. and Cox, H.K., (Eds.) Computer-aided molecular design: Applications in agrochemicals, materials and pharmaceuticals, ACS Symposium series 589, American Chemical Society, Washington, DC, 1995, pp. 82-97.
-
(1995)
ACS Symposium Series
, vol.589
, pp. 82-97
-
-
Bohacek, R.S.1
McMartin, C.2
-
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. and Marshall, G.R., VALIDATE: A new method for the receptor-based prediction of binding affinities of novel ligands, J. Am. Chem. Soc., 118 (1996) 3959-3969.
-
(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
-
-
0029000922
-
Prediction of drug binding affinities by comparative binding energy analysis
-
Ortiz, A.R., Pisabarro, M.T., Gago, F. and Wade, R.C., Prediction of drug binding affinities by comparative binding energy analysis, J. Med. Chem., 38 (1995) 2681-2691.
-
(1995)
J. Med. Chem.
, vol.38
, pp. 2681-2691
-
-
Ortiz, A.R.1
Pisabarro, M.T.2
Gago, F.3
Wade, R.C.4
-
19
-
-
0028102849
-
Effect of conformational flexibility and salvation on receptor-ligand binding free energies
-
Vajda, S., Weng, Z., Rosenfeld, R. and DeLisi, C., Effect of conformational flexibility and salvation on receptor-ligand binding free energies, Biochemistry, 33 (1994) 13977-13988.
-
(1994)
Biochemistry
, vol.33
, pp. 13977-13988
-
-
Vajda, S.1
Weng, Z.2
Rosenfeld, R.3
DeLisi, C.4
-
20
-
-
0029940017
-
Empirical free-energy as a target function in docking and design: Application to HlV-1 protease inhibitors
-
King, B.L., Vajda, S. and Delisi, C., Empirical free-energy as a target function in docking and design: Application to HlV-1 protease inhibitors, FEBS Lett., 384 (1996) 87-91.
-
(1996)
FEBS Lett.
, vol.384
, pp. 87-91
-
-
King, B.L.1
Vajda, S.2
Delisi, C.3
-
21
-
-
0028325249
-
Molecular modeling studies on ligand-binding to sialidase from influenza virus and the mechanism of catalysis
-
Taylor, N.R. and von Itzstein, M., Molecular modeling studies on ligand-binding to sialidase from influenza virus and the mechanism of catalysis, J. Med. Chem., 37 (1994) 616-624.
-
(1994)
J. Med. Chem.
, vol.37
, pp. 616-624
-
-
Taylor, N.R.1
Von Itzstein, M.2
-
22
-
-
0029003606
-
Aldose reductase as a target for drug design-Molecular modeling calculations on the binding of acyclic sugar substrates to the enzyme
-
De Winter, H.L., and von Itzstein, M., Aldose reductase as a target for drug design-Molecular modeling calculations on the binding of acyclic sugar substrates to the enzyme, Biochemistry, 34 (1995) 8299-8308.
-
(1995)
Biochemistry
, vol.34
, pp. 8299-8308
-
-
De Winter, H.L.1
Von Itzstein, M.2
-
23
-
-
0001452822
-
Correlation of binding affinities with nonbonded interaction energies of thrombin-inhibitor complexes
-
Grootenhuis, P.D.J. and van Galen, P.J.M., Correlation of binding affinities with nonbonded interaction energies of thrombin-inhibitor complexes, Acta Cryst., D51 (1995) 560-566.
-
(1995)
Acta Cryst.
, vol.D51
, pp. 560-566
-
-
Grootenhuis, P.D.J.1
Van Galen, P.J.M.2
-
24
-
-
0028519286
-
Prediction of New Serine Proteinase Inhibitors
-
Kurinov, I.V. and Harrison, R. W., Prediction of New Serine Proteinase Inhibitors, Structural Biology, 1 (1994) 735-743.
-
(1994)
Structural Biology
, vol.1
, pp. 735-743
-
-
Kurinov, I.V.1
Harrison, R.W.2
-
25
-
-
0026438932
-
Molecular mechanics analysis of inhibitor binding to HlV-1 protease
-
Sansom, C.E., Wu, J. and Weber, I.T., Molecular mechanics analysis of inhibitor binding to HlV-1 protease, Protein Eng., 5 (1992) 659-667.
-
(1992)
Protein Eng.
, vol.5
, pp. 659-667
-
-
Sansom, C.E.1
Wu, J.2
Weber, I.T.3
-
26
-
-
0029790550
-
Molecular mechanics calculations on HIV-1 prolease with peptide-substrates correlate with experimental data
-
Weber, I.T., Harrison, R.W., Molecular mechanics calculations on HIV-1 prolease with peptide-substrates correlate with experimental data, Protein Eng., 9 (1996) 679-690.
-
(1996)
Protein Eng.
, vol.9
, pp. 679-690
-
-
Weber, I.T.1
Harrison, R.W.2
-
27
-
-
0030533267
-
Design of new inhibitors of HIV-1 aspartic protease
-
Miertus, S., Furlan. M., Tossi, A. and Romeo, D., Design of new inhibitors of HIV-1 aspartic protease, Chem. Phys., 204 (1996) 173-180.
-
(1996)
Chem. Phys.
, vol.204
, pp. 173-180
-
-
Miertus, S.1
Furlan, M.2
Tossi, A.3
Romeo, D.4
-
28
-
-
1542706596
-
Efficient inhibition of HIV-1 aspartic protease by synthetic, computer designed peptide mimetics
-
Tossi, A., Furlan, M., Antcheva, N., Romeo, D. and Miertus, S., Efficient inhibition of HIV-1 aspartic protease by synthetic, computer designed peptide mimetics. Minerva Biotec., 8 (1996) 165-171.
-
(1996)
Minerva Biotec.
, vol.8
, pp. 165-171
-
-
Tossi, A.1
Furlan, M.2
Antcheva, N.3
Romeo, D.4
Miertus, S.5
-
29
-
-
13344282748
-
An approach to rapid estimation of relative binding affinities of enzyme inhibitors: Application to peptidomimetic inhibitors of the human immunodeficiency virus type I protease
-
Viswanadhan, V.N., Reddy, M.R., Wlodawer, A., Varney. M.D. and 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 I protease, J. Med. Chem., 39 (1996) 705-712.
-
(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
-
30
-
-
0029063951
-
A priori prediction of activity for HlV-1 protease inhibitors employing energy minimization in the active site
-
Holloway, M.K., Wai, J.M., Halgren, T.A., Fitzgerald, P.M.D., Vacca, J.P., Dorsey, B.D., Levin, R. B., Thompson, W.J., Chen, L.J., Desolms, S.J., Gaffin, N., Ghosh, A.K., Giuliani, E.A., Graham, S.L., Guare, J.P., Hungate, R.W., Lyle, T.A., Sanders, W.M., Tucker, T.J., Wiggins, M., Wiscount, C.M., Woltersdorf, O.W., Young, S.D., Darke, P.L., and Zugay, J.A., A priori prediction of activity for HlV-1 protease inhibitors employing energy minimization in the active site, J. Med. Chem., 38 (1995) 305-317.
-
(1995)
J. Med. Chem.
, vol.38
, pp. 305-317
-
-
Holloway, M.K.1
Wai, J.M.2
Halgren, T.A.3
Fitzgerald, P.M.D.4
Vacca, J.P.5
Dorsey, B.D.6
Levin, R.B.7
Thompson, W.J.8
Chen, L.J.9
Desolms, S.J.10
Gaffin, N.11
Ghosh, A.K.12
Giuliani, E.A.13
Graham, S.L.14
Guare, J.P.15
Hungate, R.W.16
Lyle, T.A.17
Sanders, W.M.18
Tucker, T.J.19
Wiggins, M.20
Wiscount, C.M.21
Woltersdorf, O.W.22
Young, S.D.23
Darke, P.L.24
Zugay, J.A.25
more..
-
31
-
-
0039837427
-
Structure-based design of human immunodeficiency virus-1 protease inhibitors: Correlating calculated energy with activity
-
Reynolds, C.H., Holloway, M.K., and Cox, H.K. (Eds.) Computer-aided molecular design: Applications in agrochernicals, materials, and pharmaceuticals, American Chemical Society, Washington, DC
-
Holloway, M.K. and Wai, J.M., Structure-based design of human immunodeficiency virus-1 protease inhibitors: Correlating calculated energy with activity, In Reynolds, C.H., Holloway, M.K., and Cox, H.K. (Eds.) Computer-aided molecular design: Applications in agrochernicals, materials, and pharmaceuticals, ACS Symposium series 589, American Chemical Society, Washington, DC, 1995, pp. 36-50.
-
(1995)
ACS Symposium Series
, vol.589
, pp. 36-50
-
-
Holloway, M.K.1
Wai, J.M.2
-
32
-
-
0026627809
-
Synthesis and antiviral activity of a series of HIV-1 protease inhibitors with functionality tethered to the P1 or P1, phenyl sustituents: X-ray crystal structure assisted design
-
Thompson, W.J., Fitzgerald, P.M.D., Holloway, M.K., Emini, E.A., Darke, P.L., McKeever, B.M., Schleif, W.A., Quintero, J.C., Zugay, J.A., Tucker, T.J., Schwering, J.E., Homnick, C.F., Nunberg, J., Springer, J.P. and Huff, J.R., Synthesis and antiviral activity of a series of HIV-1 protease inhibitors with functionality tethered to the P1 or P1, phenyl sustituents: X-ray crystal structure assisted design, J. Med. Chem., 35 (1992) 1685-1701.
-
(1992)
J. Med. Chem.
, vol.35
, pp. 1685-1701
-
-
Thompson, W.J.1
Fitzgerald, P.M.D.2
Holloway, M.K.3
Emini, E.A.4
Darke, P.L.5
McKeever, B.M.6
Schleif, W.A.7
Quintero, J.C.8
Zugay, J.A.9
Tucker, T.J.10
Schwering, J.E.11
Homnick, C.F.12
Nunberg, J.13
Springer, J.P.14
Huff, J.R.15
-
33
-
-
0021762055
-
Effect of pH on the activities of Penicillopepsin and Rhizopus pepsin and a proposal for the productive substrate binding mode in Penicillopepsin
-
Hofmann, T., Hodges, R.S. and James, M.N.G., Effect of pH on the activities of Penicillopepsin and Rhizopus pepsin and a proposal for the productive substrate binding mode in Penicillopepsin, Biochemistry, 23 (1984) 635-643.
-
(1984)
Biochemistry
, vol.23
, pp. 635-643
-
-
Hofmann, T.1
Hodges, R.S.2
James, M.N.G.3
-
34
-
-
0026005186
-
Human immunodeficiency virus-1 protease: 2. Use of pH rate studies and solvent kinetic isotope effects to elucidate details of chemical mechanism
-
Hyland, L.J., Tomaszek, T.A., Jr. and Meek, T.D., Human immunodeficiency virus-1 protease: 2. Use of pH rate studies and solvent kinetic isotope effects to elucidate details of chemical mechanism, Biochemistry, 30 (1991) 8454-8463.
-
(1991)
Biochemistry
, vol.30
, pp. 8454-8463
-
-
Hyland, L.J.1
Tomaszek Jr., T.A.2
Meek, T.D.3
-
35
-
-
1542601613
-
-
available from Molecular Simulations, Inc., Burlington, MA, U.S.A.
-
CHARMm version 21.1.7b.; available from Molecular Simulations, Inc., Burlington, MA, U.S.A.
-
CHARMm Version 21.1.7b
-
-
-
36
-
-
1542392018
-
-
Available from W. Clark Still, Department of Chemistry, Columbia University, New York, U.S.A..
-
Available from W. Clark Still, Department of Chemistry, Columbia University, New York, U.S.A..
-
-
-
-
38
-
-
0028057975
-
Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors
-
Lam, P.Y.S., Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors, Science, 263 (1994) 380-384.
-
(1994)
Science
, vol.263
, pp. 380-384
-
-
Lam, P.Y.S.1
-
40
-
-
0028350318
-
Conformationally constrained HIV-1 protease inhibitors
-
Vacca, J.P., Fitzgerald, P.M.D., Holloway, M.K., Hungate, R.W., Starbuck, K.E., Chen, L.J., Darke, P.L., Anderson, P.S., and Huff, J.R., Conformationally constrained HIV-1 protease inhibitors, Bioorg. Med. Chem. Lett., 4 (1994) 499-504.
-
(1994)
Bioorg. Med. Chem. Lett.
, vol.4
, pp. 499-504
-
-
Vacca, J.P.1
Fitzgerald, P.M.D.2
Holloway, M.K.3
Hungate, R.W.4
Starbuck, K.E.5
Chen, L.J.6
Darke, P.L.7
Anderson, P.S.8
Huff, J.R.9
-
41
-
-
0028017685
-
Structure- based design of HIV-1 protease inhibitors: Replacement of two amides and a 10Π-aromatic system by a fused bis-tetrahydrofuran
-
Ghosh, A.K., Thompson, W.J., Fitzgerald, P.M.D., Culberson, J.C., Axel, M.G., McKee, S.P., Huff, J.R. and Anderson, P.S., Structure-based design of HIV-1 protease inhibitors: Replacement of two amides and a 10Π-aromatic system by a fused bis-tetrahydrofuran, J. Med. Chem., 37 (1994) 2506-2508.
-
(1994)
J. Med. Chem.
, vol.37
, pp. 2506-2508
-
-
Ghosh, A.K.1
Thompson, W.J.2
Fitzgerald, P.M.D.3
Culberson, J.C.4
Axel, M.G.5
McKee, S.P.6
Huff, J.R.7
Anderson, P.S.8
-
42
-
-
0027943157
-
Crystal structure at 1.9-A resolution of human immunodeficiency virus (HlV) II protease complexed with L-735,524; An orally bioavailable inhibitor of the HIV protease
-
Chen, Z., Li, Y., Chen, E., Hall, D.L., Darke, P.L, Culberson, J.C., Shafer, J. and Kuo, L.C., Crystal structure at 1.9-A resolution of human immunodeficiency virus (HlV) II protease complexed with L-735,524; An orally bioavailable inhibitor of the HIV protease, J. Biol. Chem., 269 (1994) 26344-26348.
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 26344-26348
-
-
Chen, Z.1
Li, Y.2
Chen, E.3
Hall, D.L.4
Darke, P.L.5
Culberson, J.C.6
Shafer, J.7
Kuo, L.C.8
|