-
1
-
-
0001650642
-
-
Blaney, J. M.; Dixon, J. S. A Good Ligand Is Hard to Find: Automated Docking Methods. Perspect. Drug Discovery Des. 1993, 1, 301-319.
-
Blaney, J. M.; Dixon, J. S. A Good Ligand Is Hard to Find: Automated Docking Methods. Perspect. Drug Discovery Des. 1993, 1, 301-319.
-
-
-
-
2
-
-
0028213323
-
Theory of Macromolecule-ligand Interactions
-
Kollman, P. A. Theory of Macromolecule-ligand Interactions. Curr. Opin. Struct. Biol. 1994, 4, 240-245.
-
(1994)
Curr. Opin. Struct. Biol
, vol.4
, pp. 240-245
-
-
Kollman, P.A.1
-
3
-
-
0029623184
-
-
Ajay; Murcko, M. A. Computational Methods to Predict Binding Free Energy in Ligand-receptor Complexes. J. Med. Chem. 1995, 38, 4953-4967.
-
Ajay; Murcko, M. A. Computational Methods to Predict Binding Free Energy in Ligand-receptor Complexes. J. Med. Chem. 1995, 38, 4953-4967.
-
-
-
-
4
-
-
11644261806
-
Automated Docking using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function
-
Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated Docking using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function. J. Comput. Chem. 1998, 19, 1639-1662.
-
(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
-
-
0034332970
-
DARWIN: A Program for Docking Flexible Molecules
-
Taylor, J. S.; Burnett, R. M. DARWIN: a Program for Docking Flexible Molecules. Proteins: Struct., Funct., Genet. 2000, 41, 173-191.
-
(2000)
Proteins: Struct., Funct., Genet
, vol.41
, pp. 173-191
-
-
Taylor, J.S.1
Burnett, R.M.2
-
6
-
-
0035342434
-
High Throughput Docking for Library Design and Library Prioritization
-
Diller, D. J.; Merz, K. M., Jr. High Throughput Docking for Library Design and Library Prioritization. Proteins: Struct., Funct., Genet. 2001, 43, 113-124.
-
(2001)
Proteins: Struct., Funct., Genet
, vol.43
, pp. 113-124
-
-
Diller, D.J.1
Merz Jr., K.M.2
-
7
-
-
0033536456
-
Inclusion of Solvation in Ligand Binding Free Energy Calculations using the Generalized-born Model
-
Zou, X.; Sun, Y.; Kuntz, I. D. Inclusion of Solvation in Ligand Binding Free Energy Calculations using the Generalized-born Model. J. Am. Chem. Soc. 1999, 121, 8033-8043.
-
(1999)
J. Am. Chem. Soc
, vol.121
, pp. 8033-8043
-
-
Zou, X.1
Sun, Y.2
Kuntz, I.D.3
-
8
-
-
0035254951
-
Efficient Electrostatic Solvation Model for Protein-fragment Docking
-
Majeux, N.; Scarsi, M.; Caflisch, A. Efficient Electrostatic Solvation Model for Protein-fragment Docking. Proteins: Struct., Funct., Genet. 2001, 42, 256-268.
-
(2001)
Proteins: Struct., Funct., Genet
, vol.42
, pp. 256-268
-
-
Majeux, N.1
Scarsi, M.2
Caflisch, A.3
-
9
-
-
0025048105
-
Molecular Dynamics Simulations in Biology
-
Karplus, M.; Petsko, G. A. Molecular Dynamics Simulations in Biology. Nature 1990, 347, 631-639.
-
(1990)
Nature
, vol.347
, pp. 631-639
-
-
Karplus, M.1
Petsko, G.A.2
-
10
-
-
0000848422
-
Molecular Dynamics Computer Simulation. Method, Application and Perspectives in Chemistry
-
Van Gunsteren, W. F.; Berendsen, H. J. C. Molecular Dynamics Computer Simulation. Method, Application and Perspectives in Chemistry. Angew. Chem. 1990, 102, 1020-1055.
-
(1990)
Angew. Chem
, vol.102
, pp. 1020-1055
-
-
Van Gunsteren, W.F.1
Berendsen, H.J.C.2
-
11
-
-
0009590921
-
Free Energy Calculations: A Breakthrough for Modeling Organic Chemistry in Solution
-
Jorgensen, W. L. Free Energy Calculations: a Breakthrough for Modeling Organic Chemistry in Solution. Acc. Chem. Res. 1989, 22, 184-189.
-
(1989)
Acc. Chem. Res
, vol.22
, pp. 184-189
-
-
Jorgensen, W.L.1
-
12
-
-
7044239742
-
Free Energy Calculations: Application to Chemical and Biochemical Phenomena
-
Kollman, P. A. Free Energy Calculations: Application to Chemical and Biochemical Phenomena. Chem. Rev. 1993, 93, 2395-2417.
-
(1993)
Chem. Rev
, vol.93
, pp. 2395-2417
-
-
Kollman, P.A.1
-
13
-
-
36449007976
-
The Effect of Long-Range Electrostatic Interactions in Simulations of Macromolecular Crystals: A Comparison of Ewald and Truncated List Methods
-
York, D. M.; Darden, T. A.; Pedersen, L. G. The Effect of Long-Range Electrostatic Interactions in Simulations of Macromolecular Crystals: a Comparison of Ewald and Truncated List Methods. J. Phys. Chem. 1993, 99, 8345-8348.
-
(1993)
J. Phys. Chem
, vol.99
, pp. 8345-8348
-
-
York, D.M.1
Darden, T.A.2
Pedersen, L.G.3
-
14
-
-
11944270178
-
Cation-pi Interactions - Nonadditive Effects are Critical in Their Accurate Representation
-
Caldwell, J. W.; Kollman, P. A. Cation-pi Interactions - Nonadditive Effects are Critical in Their Accurate Representation. J. Am. Chem. Soc. 1995, 117, 4177-4178.
-
(1995)
J. Am. Chem. Soc
, vol.117
, pp. 4177-4178
-
-
Caldwell, J.W.1
Kollman, P.A.2
-
15
-
-
0028155689
-
A New Method for Predicting Binding Affinity in Computer-aided Drug Design
-
Aqvist, J.; Medina, C.; Samuelsson, J.-E. A New Method for Predicting Binding Affinity in Computer-aided Drug Design. Protein Eng. 1994, 7, 385-391.
-
(1994)
Protein Eng
, vol.7
, pp. 385-391
-
-
Aqvist, J.1
Medina, C.2
Samuelsson, J.-E.3
-
16
-
-
0001389474
-
An Extended Linear Response Method for Determining Free Energies of Hydration
-
Carlson, H. A.; Jorgensen, W. L. An Extended Linear Response Method for Determining Free Energies of Hydration. J. Phys. Chem. 1995, 99, 10667-.
-
(1995)
J. Phys. Chem
, vol.99
, pp. 10667
-
-
Carlson, H.A.1
Jorgensen, W.L.2
-
17
-
-
0029557441
-
Estimation of Binding Free Energies for HIV Protease Inhibitors by Molecular Dynamics Simulations
-
Hansson, T.; Aqvist, J. Estimation of Binding Free Energies for HIV Protease Inhibitors by Molecular Dynamics Simulations. Protein Eng. 1995, 8, 1137-1144.
-
(1995)
Protein Eng
, vol.8
, pp. 1137-1144
-
-
Hansson, T.1
Aqvist, J.2
-
18
-
-
15644376141
-
Cyclic HIV-1 Protease Inhibitors Derived from Mannitol: Synthesis, Inhibitory Potencies, and Computational Predictions of Binding Affinities
-
Hulten, J.; Bonham, N. M.; Nillroth, U.; Hansson, T.; Zuccarello, G.; Bouzide, A.; Aqvist, J.; Classon, B.; Danielson, U. H.; Karlen, A.; Kvarnstrom, I.; Samuelsson, B.; Hallberg, A. Cyclic HIV-1 Protease Inhibitors Derived from Mannitol: Synthesis, Inhibitory Potencies, and Computational Predictions of Binding Affinities. J. Med. Chem. 1997, 40, 885-97.
-
(1997)
J. Med. Chem
, vol.40
, pp. 885-897
-
-
Hulten, J.1
Bonham, N.M.2
Nillroth, U.3
Hansson, T.4
Zuccarello, G.5
Bouzide, A.6
Aqvist, J.7
Classon, B.8
Danielson, U.H.9
Karlen, A.10
Kvarnstrom, I.11
Samuelsson, B.12
Hallberg, A.13
-
19
-
-
0031637651
-
Ligand Binding Affinity Prediction by Linear Interaction Energy Methods
-
Hansson, T.; Marelius, J.; Aqvist, J. Ligand Binding Affinity Prediction by Linear Interaction Energy Methods. J. Comput.-Aided Mol. Des. 1998, 12, 27-35.
-
(1998)
J. Comput.-Aided Mol. Des
, vol.12
, pp. 27-35
-
-
Hansson, T.1
Marelius, J.2
Aqvist, J.3
-
20
-
-
0032014129
-
Computation of Affinity and Selectivity: Binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline Inhibitors to Dihydrofolate Reductases
-
Marelius, J.; Graffner-Nordberg, M.; Hansson, T.; Hallberg, A.; Aqvist, J. Computation of Affinity and Selectivity: Binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline Inhibitors to Dihydrofolate Reductases. J. Comput.-Aided Mol. Des. 1998, 12, 119-131.
-
(1998)
J. Comput.-Aided Mol. Des
, vol.12
, pp. 119-131
-
-
Marelius, J.1
Graffner-Nordberg, M.2
Hansson, T.3
Hallberg, A.4
Aqvist, J.5
-
21
-
-
0035105526
-
Computational Modelling of Inhibitor Binding to Human Thrombin
-
Ljungberg, K. B.; Marelius, J.; Musil, D.; Svensson, P.; Norden, B.; Aqvist, J. Computational Modelling of Inhibitor Binding to Human Thrombin. Eur. J. Pharm. Sci. 2001, 12, 441-446.
-
(2001)
Eur. J. Pharm. Sci
, vol.12
, pp. 441-446
-
-
Ljungberg, K.B.1
Marelius, J.2
Musil, D.3
Svensson, P.4
Norden, B.5
Aqvist, J.6
-
22
-
-
0034925093
-
Computational Analysis of Binding of P1 Variants to Trypsin
-
Brandsdal, B. O.; Aqvist, J.; Smalas, A. O. Computational Analysis of Binding of P1 Variants to Trypsin. Protein Sci. 2001, 10, 1584-1595.
-
(2001)
Protein Sci
, vol.10
, pp. 1584-1595
-
-
Brandsdal, B.O.1
Aqvist, J.2
Smalas, A.O.3
-
23
-
-
0001127721
-
Free Energies of Solvation in Chloroform and Water from a Linear Response Approach
-
McDonald, H.; Carlson, A.; Jorgensen, W. L. Free Energies of Solvation in Chloroform and Water from a Linear Response Approach. J. Phys. Org. Chem. 1997, 10, 563-576.
-
(1997)
J. Phys. Org. Chem
, vol.10
, pp. 563-576
-
-
McDonald, H.1
Carlson, A.2
Jorgensen, W.L.3
-
24
-
-
0030906731
-
Binding Affinities for Sulfonamide Inhibitors with Human Thrombin using Monte Carlo Simulations with a Linear Response Method
-
Jones-Hertzog, D. K.; Jorgensen, W. L. Binding Affinities for Sulfonamide Inhibitors with Human Thrombin using Monte Carlo Simulations with a Linear Response Method. J. Med. Chem. 1997, 40, 1539-1549.
-
(1997)
J. Med. Chem
, vol.40
, pp. 1539-1549
-
-
Jones-Hertzog, D.K.1
Jorgensen, W.L.2
-
25
-
-
20644437755
-
Prediction of Binding Affinities for TIBO Inhibitors of HIV-1 Reverse Transcriptase using Monte Carlo Simulations in a Linear Response Method
-
Smith, R. H., Jr.; Jorgensen, W. L.; Tirado-Rives, J.; Lamb, M. L.; Janssen, P. A. J.; Michejda, C. J.; Smith, M. B. K. Prediction of Binding Affinities for TIBO Inhibitors of HIV-1 Reverse Transcriptase using Monte Carlo Simulations in a Linear Response Method. J. Med. Chem. 1998, 41, 5272-5286.
-
(1998)
J. Med. Chem
, vol.41
, pp. 5272-5286
-
-
Smith Jr., R.H.1
Jorgensen, W.L.2
Tirado-Rives, J.3
Lamb, M.L.4
Janssen, P.A.J.5
Michejda, C.J.6
Smith, M.B.K.7
-
26
-
-
0033135425
-
Estimation of the Binding Affinities of FKBP12 Inhibitors using a Linear Response Method
-
Lamb, M. L.; Tirado-Rives, J.; Jorgensen, W. L. Estimation of the Binding Affinities of FKBP12 Inhibitors using a Linear Response Method. Bioorg. Med. Chem. 1999, 7, 851-860.
-
(1999)
Bioorg. Med. Chem
, vol.7
, pp. 851-860
-
-
Lamb, M.L.1
Tirado-Rives, J.2
Jorgensen, W.L.3
-
27
-
-
0035950792
-
New Linear Interaction Method for Binding Affinity Calculations using a Continuum Solvent Model
-
Zhou, R.; Friesner, R. A.; Ghosh, A.; Rizzo, R. C.; Jorgensen, W. L.; Levy, R. M. New Linear Interaction Method for Binding Affinity Calculations using a Continuum Solvent Model. J. Phys. Chem. B 2001, 105, 10388-10397.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 10388-10397
-
-
Zhou, R.1
Friesner, R.A.2
Ghosh, A.3
Rizzo, R.C.4
Jorgensen, W.L.5
Levy, R.M.6
-
28
-
-
0346052295
-
A Generalized Linear Response Method: Application to the Hydration Free Energy Calculations
-
Chen, X.; Tropsha, A. A Generalized Linear Response Method: Application to the Hydration Free Energy Calculations. J. Comput. Chem. 1999, 20, 749-759.
-
(1999)
J. Comput. Chem
, vol.20
, pp. 749-759
-
-
Chen, X.1
Tropsha, A.2
-
29
-
-
0001672288
-
Chemical and Electrochemical Electron-transfer Theory
-
Marcus, R. A. Chemical and Electrochemical Electron-transfer Theory. Annu. Rev. Phys. Chem. 1964, 15, 155-196.
-
(1964)
Annu. Rev. Phys. Chem
, vol.15
, pp. 155-196
-
-
Marcus, R.A.1
-
30
-
-
0026596911
-
Calculations of Antibody-antigen Interactions: Microscopic and Semi-microscopic Evaluation of the Free Energies of Binding of Phosphorylcholine Analogs to McPC603
-
Lee, F. S.; Chu, Z.-T.; Bolger, M. B.; Warshel, A. Calculations of Antibody-antigen Interactions: Microscopic and Semi-microscopic Evaluation of the Free Energies of Binding of Phosphorylcholine Analogs to McPC603. Protein Eng. 1992, 5, 215-228.
-
(1992)
Protein Eng
, vol.5
, pp. 215-228
-
-
Lee, F.S.1
Chu, Z.-T.2
Bolger, M.B.3
Warshel, A.4
-
31
-
-
0242677212
-
Calculation of Electrostatic Free Energy Differences with a Time-saving Approximate Method
-
King, G.; Barford, R. A. Calculation of Electrostatic Free Energy Differences with a Time-saving Approximate Method. J. Phys. Chem. 1993, 97, 8798-8802.
-
(1993)
J. Phys. Chem
, vol.97
, pp. 8798-8802
-
-
King, G.1
Barford, R.A.2
-
32
-
-
0006165024
-
Analysis of Coupling Schemes in Free energy Simulations: A Unified Description of Nonbonded Contribution to Solvation Free Energies
-
Dejaegere, A.; Karplus, M. Analysis of Coupling Schemes in Free energy Simulations: a Unified Description of Nonbonded Contribution to Solvation Free Energies. J. Phys. Chem. 1996, 100, 11148-11164.
-
(1996)
J. Phys. Chem
, vol.100
, pp. 11148-11164
-
-
Dejaegere, A.1
Karplus, M.2
-
33
-
-
33747754400
-
-
Pierotti, R. A. A Scaled Particle Theory of Aqueous and Nonaqueous Solutions. Chem. Rev. 1976, 76, 717-726.
-
Pierotti, R. A. A Scaled Particle Theory of Aqueous and Nonaqueous Solutions. Chem. Rev. 1976, 76, 717-726.
-
-
-
-
34
-
-
0004067382
-
-
Reidel: Dordrecht, Holland
-
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. Intermolecular Forces; Reidel: Dordrecht, Holland, 1981.
-
(1981)
Intermolecular Forces
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
van Gunsteren, W.F.3
Hermans, J.4
-
35
-
-
0026503819
-
Application of Free Energy Simulations to the Binding of a Transition-state-analogue Inhibitor to HIV Protease
-
Tropsha, A.; Hermans, J. Application of Free Energy Simulations to the Binding of a Transition-state-analogue Inhibitor to HIV Protease. Protein Eng. 1992, 5, 29-33.
-
(1992)
Protein Eng
, vol.5
, pp. 29-33
-
-
Tropsha, A.1
Hermans, J.2
-
36
-
-
0026047763
-
Determination of the Relative Binding Free Energies of Peptide Inhibitors to the HIV-1 Protease
-
Ferguson, D. M.; Radmer, R. J.; Kollman, P. A. Determination of the Relative Binding Free Energies of Peptide Inhibitors to the HIV-1 Protease. J. Med. Chem. 1991, 34, 2654-2659.
-
(1991)
J. Med. Chem
, vol.34
, pp. 2654-2659
-
-
Ferguson, D.M.1
Radmer, R.J.2
Kollman, P.A.3
-
37
-
-
0025720738
-
Relative Differences in the Binding Free Energies of Human Immunodeficiency Virus 1 Protease Inhibitors: A Thermodynamic Cycle-perturbation Approach
-
Reddy, M. R.; Viswanadhan, V. N.; Weinstein, J. N. Relative Differences in the Binding Free Energies of Human Immunodeficiency Virus 1 Protease Inhibitors: a Thermodynamic Cycle-perturbation Approach. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 10287-10291.
-
(1991)
Proc. Natl. Acad. Sci. U.S.A
, vol.88
, pp. 10287-10291
-
-
Reddy, M.R.1
Viswanadhan, V.N.2
Weinstein, J.N.3
-
38
-
-
0025829331
-
Structure at 2.5-.ANG. Resolution of Chemically Synthesized Human Immunodeficiency Virus Type 1 Protease Complexed with a Hydroxyethylene-based Inhibitor
-
Jaskolski, M.; Tomasselli, A. G.; Sawyer, T. K.; Staples, D. G.; Heinrikson, R. L.; Schneider, J.; Kent, S. B. H.; Wlodawer, A. Structure at 2.5-.ANG. Resolution of Chemically Synthesized Human Immunodeficiency Virus Type 1 Protease Complexed with a Hydroxyethylene-based Inhibitor. Biochemistry 1991, 30, 1600-1609.
-
(1991)
Biochemistry
, vol.30
, pp. 1600-1609
-
-
Jaskolski, M.1
Tomasselli, A.G.2
Sawyer, T.K.3
Staples, D.G.4
Heinrikson, R.L.5
Schneider, J.6
Kent, S.B.H.7
Wlodawer, A.8
-
39
-
-
1542676148
-
-
University of North Carolina at Chapel Hill
-
Hermans, J. Sigma Manual; University of North Carolina at Chapel Hill, 1994.
-
(1994)
Sigma Manual
-
-
Hermans, J.1
-
40
-
-
84990424072
-
-
Hermans, J.; Berendsen, H. J. C.; van Gunsteren, W. F.; Postma, J. P. M. A Consistent Empirical Potential for Water-protein Interactions. Biopolymers 1984, 23, 1513-1518.
-
Hermans, J.; Berendsen, H. J. C.; van Gunsteren, W. F.; Postma, J. P. M. A Consistent Empirical Potential for Water-protein Interactions. Biopolymers 1984, 23, 1513-1518.
-
-
-
-
41
-
-
0019316782
-
Energy Minimizations of Rubredoxin
-
Ferro, D. R.; McQueen, J. E.; McCown, J. T.; Hermans, J. Energy Minimizations of Rubredoxin. J. Mol. Biol. 1980, 136, 1-18.
-
(1980)
J. Mol. Biol
, vol.136
, pp. 1-18
-
-
Ferro, D.R.1
McQueen, J.E.2
McCown, J.T.3
Hermans, J.4
-
42
-
-
84986469434
-
A Method for Constrained Energy Minimization of Macromolecules
-
Van Gunsteren, W. F.; Karplus, M. A Method for Constrained Energy Minimization of Macromolecules. J. Comput. Chem. 1980, 1, 266-274.
-
(1980)
J. Comput. Chem
, vol.1
, pp. 266-274
-
-
Van Gunsteren, W.F.1
Karplus, M.2
-
43
-
-
0025774665
-
Effect of Hydroxyl Group Configuration in Hydroxyethylamine Dipeptide Isosteres on HIV Protease Inhibition - Evidence for Multiple Binding Modes
-
Rich, D. H.; Sun, C. Q.; Vara Prasad, J. V. N.; Pathiasseril, A.; Toth, M. V.; Marshall, G. R.; Clare, M.; Mueller, R. A.; Houseman, K. Effect of Hydroxyl Group Configuration in Hydroxyethylamine Dipeptide Isosteres on HIV Protease Inhibition - Evidence for Multiple Binding Modes. J. Med. Chem. 1991, 34, 1222-1225.
-
(1991)
J. Med. Chem
, vol.34
, pp. 1222-1225
-
-
Rich, D.H.1
Sun, C.Q.2
Vara Prasad, J.V.N.3
Pathiasseril, A.4
Toth, M.V.5
Marshall, G.R.6
Clare, M.7
Mueller, R.A.8
Houseman, K.9
-
44
-
-
0009235161
-
-
Pearlman, D. A. A Comparison of Alternative Approaches to Free Energy Calculations. J. Phy. Chem. 1994, 98, 1487-1493.
-
Pearlman, D. A. A Comparison of Alternative Approaches to Free Energy Calculations. J. Phy. Chem. 1994, 98, 1487-1493.
-
-
-
-
45
-
-
0742307009
-
HIV-1 Protease: Structure-based Drug Design Using the Free Energy Perturbation Approach
-
Reddy, M. R.; Appelt, K. HIV-1 Protease: Structure-based Drug Design Using the Free Energy Perturbation Approach. Free Energy Calculations Rational Drug Des. 2001, 317-334.
-
(2001)
Free Energy Calculations Rational Drug Des
, pp. 317-334
-
-
Reddy, M.R.1
Appelt, K.2
-
46
-
-
0342321950
-
Examining Methods for Calculations of Binding Free Energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA Calculations of Ligands Binding to an HIV Protease
-
Sham, Y. Y.; Chu, Z. T.; Tao, H.; Warshel, A. Examining Methods for Calculations of Binding Free Energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA Calculations of Ligands Binding to an HIV Protease. Proteins: Struct., Funct., Genet. 2000, 39, 393-407.
-
(2000)
Proteins: Struct., Funct., Genet
, vol.39
, pp. 393-407
-
-
Sham, Y.Y.1
Chu, Z.T.2
Tao, H.3
Warshel, A.4
|