-
1
-
-
0017411710
-
The Protein Data Bank: A computer-based archival file for macromolecular structures
-
Bernstein, F. C.; Koetzle, T. F.; Williams, G. J. B.; Meyer Jr., E. F.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 1977, 112, 535-542.
-
(1977)
J. Mol. Biol.
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
Meyer Jr., E.F.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
2
-
-
0036606483
-
Principles of Docking: An Overview of Search Algorithms and a Guide to Scoring Functions
-
Halperin, I.; Ma, B.; Wolfson, H.; Nussinov, R. Principles of Docking: An Overview of Search Algorithms and a Guide to Scoring Functions. Proteins 2002, 47, 409-443.
-
(2002)
Proteins
, vol.47
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
3
-
-
0036520840
-
A Review of Protein-Small Molecule Docking Methods
-
Taylor, R. D.; Jewsbury, P. J.; Essex, J. W. A Review of Protein-Small Molecule Docking Methods. J. Comput.-Aided Mol. Design 2002, 16, 151-166.
-
(2002)
J. Comput.-Aided Mol. Design
, vol.16
, pp. 151-166
-
-
Taylor, R.D.1
Jewsbury, P.J.2
Essex, J.W.3
-
4
-
-
0037262054
-
Ligand-Protein Docking: Cancer Research at the Interface between Biology and Chemistry
-
Glen, R. C.; Allen, S. C. Ligand-Protein Docking: Cancer Research at the Interface between Biology and Chemistry. Current Medicinal Chemistry 2003, 10, 763-777.
-
(2003)
Current Medicinal Chemistry
, vol.10
, pp. 763-777
-
-
Glen, R.C.1
Allen, S.C.2
-
5
-
-
0037008160
-
Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors
-
Gohlke, H.; Klebe, G. Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors. Angew. Chem. Int. Ed. 2002, 41, 2644-2676.
-
(2002)
Angew. Chem. Int. Ed.
, vol.41
, pp. 2644-2676
-
-
Gohlke, H.1
Klebe, G.2
-
6
-
-
0036589890
-
Structure-based Approaches to Drug Design and Virtual Screening
-
Waszkowycz, B. Structure-based Approaches to Drug Design and Virtual Screening. Curr. Opin. Drug. Discov. Dev. 2002, 5, 407-413.
-
(2002)
Curr. Opin. Drug. Discov. Dev.
, vol.5
, pp. 407-413
-
-
Waszkowycz, B.1
-
7
-
-
0036007208
-
Virtual Screening and Fast Automated Docking Methods
-
Schneider, G.; Böhm, H.-J. Virtual Screening and Fast Automated Docking Methods. Drug Discov. Today 2002, 7, 64-70.
-
(2002)
Drug Discov. Today
, vol.7
, pp. 64-70
-
-
Schneider, G.1
Böhm, H.-J.2
-
8
-
-
0037107887
-
Structure-based Virtual Screening: An Overview
-
Lyric, P.D. Structure-based Virtual Screening: An Overview. Drug Discov. Today 2002, 7, 1047-1055.
-
(2002)
Drug Discov. Today
, vol.7
, pp. 1047-1055
-
-
Lyric, P.D.1
-
9
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank. Nucl. Acids Res. 2000, 28, 235-242.
-
(2000)
Nucl. Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
10
-
-
0037436339
-
Relibase: Design and Development of a Database for Comprehensive Analysis of Protein-Ligand Interactions
-
Hendlich, M.; Bergner, A.; Günther, J.; Klebe, G. Relibase: Design and Development of a Database for Comprehensive Analysis of Protein-Ligand Interactions. J. Mol. Biol. 2003, 326, 607-620.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 607-620
-
-
Hendlich, M.1
Bergner, A.2
Günther, J.3
Klebe, G.4
-
11
-
-
84892166712
-
Einfluss der Konfiguration auf die Wirkung der Enzyme
-
Fischer, E. Einfluss der Konfiguration auf die Wirkung der Enzyme. Ber. Dtsch. Chem. Ges. 1894, 27, 2985-2993.
-
(1894)
Ber. Dtsch. Chem. Ges.
, vol.27
, pp. 2985-2993
-
-
Fischer, E.1
-
12
-
-
0020491251
-
A Geometric Approach to Macromolecule-Ligand Interactions
-
Kuntz, I. D.; Blaney, J. M.; Oatley, S. J.; Langridge, R.; Ferrin, T. E. A Geometric Approach to Macromolecule-Ligand Interactions. J. Mol. Biol. 1982, 161, 269-288.
-
(1982)
J. Mol. Biol.
, vol.161
, pp. 269-288
-
-
Kuntz, I.D.1
Blaney, J.M.2
Oatley, S.J.3
Langridge, R.4
Ferrin, T.E.5
-
13
-
-
0026570977
-
CLIX: A Search Algorithm for Finding Novel Ligands Capable of Binding Proteins of Known Three-Dimensional Structure
-
Lawrence, M. C.; Davis, P. C. CLIX: A Search Algorithm for Finding Novel Ligands Capable of Binding Proteins of Known Three-Dimensional Structure. Proteins 1992, 12, 31-41.
-
(1992)
Proteins
, vol.12
, pp. 31-41
-
-
Lawrence, M.C.1
Davis, P.C.2
-
14
-
-
84986467005
-
Conformational Analysis of Flexible Ligands in Macromolecular Receptor Sites
-
Leach, A. R.; Kuntz, I. D. Conformational Analysis of Flexible Ligands in Macromolecular Receptor Sites. J. Comput. Chem. 1992, 13, 730-748.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 730-748
-
-
Leach, A.R.1
Kuntz, I.D.2
-
15
-
-
0027385177
-
Matching Chemistry and Shape in Molecular Docking
-
Shoichet, B. K.; Kuntz, I. D. Matching Chemistry and Shape in Molecular Docking. Protein Eng. 1993, 6, 223-232.
-
(1993)
Protein Eng.
, vol.6
, pp. 223-232
-
-
Shoichet, B.K.1
Kuntz, I.D.2
-
16
-
-
0028412035
-
FLOG: A System to Select 'Quasi-Flexible' Ligands Complementary to a Receptor of Known Three-Dimensional Structure
-
Miller, M. D.; Kearsley, S. K.; Underwood, D. J.; Sheridan, R. P. FLOG: A System to Select 'Quasi-Flexible' Ligands Complementary to a Receptor of Known Three-Dimensional Structure. J. Comput.-Aided Mol. Design 1994, 8, 153-174.
-
(1994)
J. Comput.-Aided Mol. Design
, vol.8
, pp. 153-174
-
-
Miller, M.D.1
Kearsley, S.K.2
Underwood, D.J.3
Sheridan, R.P.4
-
17
-
-
0028452628
-
A Shape- and Chemistry-based Docking Method and its Use in the Design of HIV-1 Protease Inhibitors
-
DesJarlais, R. L.; Dixon, J. S. A Shape- and Chemistry-based Docking Method and its Use in the Design of HIV-1 Protease Inhibitors. J. Comput.-Aided Mol. Design 1994, 8, 231-242.
-
(1994)
J. Comput.-Aided Mol. Design
, vol.8
, pp. 231-242
-
-
DesJarlais, R.L.1
Dixon, J.S.2
-
18
-
-
0029942661
-
Structure-derived Potentials and Protein Simulations
-
Jernigan, R. L.; Bahar, I. Structure-derived Potentials and Protein Simulations. Curr. Opin. Struct. Biol. 1996, 6, 195-209.
-
(1996)
Curr. Opin. Struct. Biol.
, vol.6
, pp. 195-209
-
-
Jernigan, R.L.1
Bahar, I.2
-
19
-
-
0036667733
-
Knowledge-based Potential Functions in Protein Design
-
Russ, W. P.; Ranganathan, R. Knowledge-based Potential Functions in Protein Design. Curr. Opin. Struct. Biol. 2002, 12, 447-452.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 447-452
-
-
Russ, W.P.1
Ranganathan, R.2
-
20
-
-
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. Prot. Sci. 1995, 4, 1881-1903.
-
(1995)
Prot. Sci.
, vol.4
, pp. 1881-1903
-
-
Wallqvist, A.1
Jernigan, R.L.2
Covell, D.G.3
-
21
-
-
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. Prot. Eng. 1995, 8, 677-691.
-
(1995)
Prot. Eng.
, vol.8
, pp. 677-691
-
-
Verkhivker, G.1
Appelt, K.2
Freer, S.T.3
Villafranca, J.E.4
-
22
-
-
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. 1996, 118, 11733-11744.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11733-11744
-
-
DeWitte, R.S.1
Shakhnovich, E.I.2
-
23
-
-
0000823044
-
BLEEP - Potential of Mean Force Describing Protein-Ligand Interactions: I. Generating Potential
-
Mitchell, J. B. O.; Laskowski, R. A.; Alex, A.; Thornton, J. M. BLEEP - Potential of Mean Force Describing Protein-Ligand Interactions: I. Generating Potential. J. Comput. Chem. 1999, 20, 1165-1176.
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 1165-1176
-
-
Mitchell, J.B.O.1
Laskowski, R.A.2
Alex, A.3
Thornton, J.M.4
-
24
-
-
0033545622
-
A General and Fast Scoring Function for Protein-Ligand Interactions: A Simplified Potential Approach
-
Muegge, I.; Martin, Y. C. A General and Fast Scoring Function for Protein-Ligand Interactions: A Simplified Potential Approach. J. Med. Chem. 1999, 42, 791-804.
-
(1999)
J. Med. Chem.
, vol.42
, pp. 791-804
-
-
Muegge, I.1
Martin, Y.C.2
-
25
-
-
0034645763
-
Knowledge-based Scoring Function to Predict Protein-Ligand Interactions
-
Gohlke, H.; Hendlich, M.; Klebe, G. Knowledge-based Scoring Function to Predict Protein-Ligand Interactions. J. Mol. Biol. 2000, 295, 337-356.
-
(2000)
J. Mol. Biol.
, vol.295
, pp. 337-356
-
-
Gohlke, H.1
Hendlich, M.2
Klebe, G.3
-
26
-
-
0037142298
-
Small Molecule Growth 2001 (SMoG2001): An Improved Knowledge-based Scoring Function for Protein-Ligand Interactions
-
Ishchenko, A. V.; Shakhnovich, E. I. Small Molecule Growth 2001 (SMoG2001): An Improved Knowledge-based Scoring Function for Protein-Ligand Interactions. J. Am. Chem. Soc. 2002, 45, 2770-2780.
-
(2002)
J. Am. Chem. Soc.
, vol.45
, pp. 2770-2780
-
-
Ishchenko, A.V.1
Shakhnovich, E.I.2
-
27
-
-
0036001094
-
From Knowledge-based Potentials to Combinatorial Lead Design in Silico
-
Grzybowski, B. A.; Ishchenko, A. V.; Shimada, J.; Shakhnovich, E. I. From Knowledge-based Potentials to Combinatorial Lead Design in Silico. Acc. Chem. Res. 2002, 35, 261-269.
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 261-269
-
-
Grzybowski, B.A.1
Ishchenko, A.V.2
Shimada, J.3
Shakhnovich, E.I.4
-
28
-
-
0037022302
-
Combinatorial Computational Method Gives New Picomolar Ligands for a Known Enzyme
-
Grzybowski, B. A.; Ishchenko, A. V.; Kim, C.-Y.; Topalov, G.; Chapman, R.; Christianson, D. W.; Whitesides, G. M.; Shakhnovich, E. I. Combinatorial Computational Method Gives New Picomolar Ligands for a Known Enzyme. Proc. Natl. Acad. Sci. 2002, 99, 1270-1273.
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 1270-1273
-
-
Grzybowski, B.A.1
Ishchenko, A.V.2
Kim, C.-Y.3
Topalov, G.4
Chapman, R.5
Christianson, D.W.6
Whitesides, G.M.7
Shakhnovich, E.I.8
-
29
-
-
0000882405
-
BLEEP - Potential of Mean Force Describing Protein-Ligand Interactions: II. Calculation of Binding Energies and Comparison with Experimental Data
-
Mitchell, J. B. O.; Laskowski, R. A.; Alex, A.; Forster, M. J.; Thornton, J. M. BLEEP - Potential of Mean Force Describing Protein-Ligand Interactions: II. Calculation of Binding Energies and Comparison with Experimental Data. J. Comput. Chem. 1999, 20, 1177-1185.
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 1177-1185
-
-
Mitchell, J.B.O.1
Laskowski, R.A.2
Alex, A.3
Forster, M.J.4
Thornton, J.M.5
-
30
-
-
0033566211
-
Evaluation of PMF Scoring in Docking Weak Ligands to the FK506 Binding Protein
-
Muegge, I.; Martin, Y. C.; Hajduk, P. J.; Fesik, S. W. Evaluation of PMF Scoring in Docking Weak Ligands to the FK506 Binding Protein. J. Med. Chem. 1999, 42, 2498-2503.
-
(1999)
J. Med. Chem.
, vol.42
, pp. 2498-2503
-
-
Muegge, I.1
Martin, Y.C.2
Hajduk, P.J.3
Fesik, S.W.4
-
31
-
-
0001745748
-
Effect of Ligand Volume Correction on PMF Scoring
-
Muegge, I. Effect of Ligand Volume Correction on PMF Scoring. J. Comput. Chem. 2001, 22, 418-425.
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 418-425
-
-
Muegge, I.1
-
32
-
-
3042610894
-
-
Sybyl Atom Types
-
Sybyl Atom Types: http://tripos.com/custResources/mol2Files/atom_types.html
-
-
-
-
33
-
-
0033668689
-
Predicting Binding Modes, Binding Affinities and 'Hot Spots' for Protein-Ligand Complexes Using a Knowledge-based Scoring Function
-
Gohlke, H.; Hendlich, M.; Klebe, G. Predicting Binding Modes, Binding Affinities and 'Hot Spots' for Protein-Ligand Complexes Using a Knowledge-based Scoring Function. Perspect. Drug. Discov. Design 2000, 20, 115-144.
-
(2000)
Perspect. Drug. Discov. Design
, vol.20
, pp. 115-144
-
-
Gohlke, H.1
Hendlich, M.2
Klebe, G.3
-
34
-
-
0035339739
-
Evaluation of a Knowledge-based Potential of Mean Force for Scoring Docked Protein-Ligand Complexes
-
Nobeli, I.; Mitchell, J. B. O.; Alex, A.; Thornton, J. M. Evaluation of a Knowledge-based Potential of Mean Force for Scoring Docked Protein-Ligand Complexes. J. Comput. Chem. 2001, 22, 673-698.
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 673-698
-
-
Nobeli, I.1
Mitchell, J.B.O.2
Alex, A.3
Thornton, J.M.4
-
35
-
-
0002192615
-
-
Kuhl, F. S.; Crippen, G. M.; Friesen, D. K. J. Comput. Chem. 1984, 5, 24-34.
-
(1984)
J. Comput. Chem.
, vol.5
, pp. 24-34
-
-
Kuhl, F.S.1
Crippen, G.M.2
Friesen, D.K.3
-
36
-
-
12444278563
-
Analysis and Optimization of Structure-based Virtual Screening Protocols. 2. Examination of Docked Ligand Orientation Sampling Methodology: Mapping a Pharmacophore for Success
-
Good, A. C.; Cheney, D. L.; Sitkoff, D. F.; Tokarski, J. S.; Stouch, T. R.; Bassolino, D. A.; Krystek, S. R.; Li, Y.; Mason, J. S.; Perkins, T. D. J. Analysis and Optimization of Structure-based Virtual Screening Protocols. 2. Examination of Docked Ligand Orientation Sampling Methodology: Mapping a Pharmacophore for Success. J. Mol. Graphics Mod. 2003, 22, 31-40.
-
(2003)
J. Mol. Graphics Mod.
, vol.22
, pp. 31-40
-
-
Good, A.C.1
Cheney, D.L.2
Sitkoff, D.F.3
Tokarski, J.S.4
Stouch, T.R.5
Bassolino, D.A.6
Krystek, S.R.7
Li, Y.8
Mason, J.S.9
Perkins, T.D.J.10
-
37
-
-
0031552362
-
Development and Validation of a Genetic Algorithm for Flexible Docking
-
Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and Validation of a Genetic Algorithm for Flexible Docking. J. Mol. Biol. 1997, 267, 727-748.
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 727-748
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
Leach, A.R.4
Taylor, R.5
-
38
-
-
0013133162
-
-
Nissink, J. W. M.; Murray, C.; Hartshorn, M.; Verdonk, M. L.; Cole, J. C.; Taylor, R. Proteins 2002, 49, 457-471.
-
(2002)
Proteins
, vol.49
, pp. 457-471
-
-
Nissink, J.W.M.1
Murray, C.2
Hartshorn, M.3
Verdonk, M.L.4
Cole, J.C.5
Taylor, R.6
-
39
-
-
0033674405
-
Virtual Screening with Solvation and Ligand-Induced Complementarity
-
Schnecke, V.; Kuhn, L. A. Virtual Screening with Solvation and Ligand-Induced Complementarity. Perspect. Drug Discov. Design 2000, 20, 171-190.
-
(2000)
Perspect. Drug Discov. Design
, vol.20
, pp. 171-190
-
-
Schnecke, V.1
Kuhn, L.A.2
-
40
-
-
0035896038
-
Docking Ligands onto Binding Site Representations Derived from Proteins built by Homology Modelling
-
Schafferhans, A.; Klebe, G. Docking Ligands onto Binding Site Representations Derived from Proteins built by Homology Modelling. J. Mol. Biol. 2001, 307, 407-427.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 407-427
-
-
Schafferhans, A.1
Klebe, G.2
-
41
-
-
44949267284
-
An Alternative Method for the Alignment of Molecular Structures: Maximizing Electrostatic and Steric Overlap
-
Kearsley, S. K.; Smith, G. M. An Alternative Method for the Alignment of Molecular Structures: Maximizing Electrostatic and Steric Overlap. Tetrahedron Comput. Methodol. 1990, 3, 615-633.
-
(1990)
Tetrahedron Comput. Methodol.
, vol.3
, pp. 615-633
-
-
Kearsley, S.K.1
Smith, G.M.2
-
42
-
-
0028722704
-
Different Approaches Toward an Automatic Structural Alignment of Drug Molecules: Application to Sterol Mimics, Thrombin and Thermolysin Inhibitors
-
Klebe, G.; Mietzner, T.; Weber, F. Different Approaches Toward an Automatic Structural Alignment of Drug Molecules: Application to Sterol Mimics, Thrombin and Thermolysin Inhibitors. J. Comput.-Aided Mol. Design 1994, 8, 751-778.
-
(1994)
J. Comput.-Aided Mol. Design
, vol.8
, pp. 751-778
-
-
Klebe, G.1
Mietzner, T.2
Weber, F.3
-
43
-
-
0001171748
-
MIMIC: A Molecular-Field Matching Program. Exploiting the Applicability of Molecular Similarity Approaches
-
Mestres, J.; Rohrer, D. C.; Maggiora, G. M. MIMIC: A Molecular-Field Matching Program. Exploiting the Applicability of Molecular Similarity Approaches. J. Comput. Chem. 1997, 18, 934-954.
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 934-954
-
-
Mestres, J.1
Rohrer, D.C.2
Maggiora, G.M.3
-
44
-
-
0346665839
-
Gaussian Docking Functions
-
McGann, M. R.; Almond, H. R.; Nicholls, A.; Grant, J. A.; Brown, F. K. Gaussian Docking Functions. Biopolymers 2003, 68, 76-90.
-
(2003)
Biopolymers
, vol.68
, pp. 76-90
-
-
McGann, M.R.1
Almond, H.R.2
Nicholls, A.3
Grant, J.A.4
Brown, F.K.5
-
45
-
-
0038185582
-
Binding Site Characteristics in Structure-based Virtual Screening: Evaluation of Current Docking Tools
-
Schulz-Gasch, T.; Stahl, M. Binding Site Characteristics in Structure-based Virtual Screening: Evaluation of Current Docking Tools. J. Mol. Madel. 2003, 9, 47-57.
-
(2003)
J. Mol. Model.
, vol.9
, pp. 47-57
-
-
Schulz-Gasch, T.1
Stahl, M.2
-
46
-
-
0030599010
-
A Fast Flexible Docking Method Using an Incremental Construction Algorithm
-
Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A Fast Flexible Docking Method Using an Incremental Construction Algorithm. J. Mol. Biol. 1996, 261, 470-489.
-
(1996)
J. Mol. Biol.
, vol.261
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
47
-
-
0032738842
-
Evaluation of the FlexX Incremental Construction Algorithm for Protein-Ligand Docking
-
Kramer, B.; Rarey, M.; Lengauer, T. Evaluation of the FlexX Incremental Construction Algorithm for Protein-Ligand Docking. Proteins 1999, 37, 228-241.
-
(1999)
Proteins
, vol.37
, pp. 228-241
-
-
Kramer, B.1
Rarey, M.2
Lengauer, T.3
-
48
-
-
0032571380
-
-
Burkhard, P.; Taylor, P.; Walkinshaw, M. D. J. Mol. Biol. 1998, 277, 449-466.
-
(1998)
J. Mol. Biol.
, vol.277
, pp. 449-466
-
-
Burkhard, P.1
Taylor, P.2
Walkinshaw, M.D.3
-
49
-
-
0036022958
-
Flexible Docking under Pharmacophore Type Constraints
-
Hindle, S. A.; Rarey, M.; Buning, C.; Lengauer, T. Flexible Docking under Pharmacophore Type Constraints. J. Comput.-Aided Mol. Design 2002, 16, 129-149.
-
(2002)
J. Comput.-Aided Mol. Design
, vol.16
, pp. 129-149
-
-
Hindle, S.A.1
Rarey, M.2
Buning, C.3
Lengauer, T.4
-
50
-
-
0021871375
-
A Computational Procedure for Determining Energetically Favorable Binding Sites on Biologically Important Macromolecules
-
Goodford, P. A. A Computational Procedure for Determining Energetically Favorable Binding Sites on Biologically Important Macromolecules. J. Med. Chem. 1985, 28, 849-857.
-
(1985)
J. Med. Chem.
, vol.28
, pp. 849-857
-
-
Goodford, P.A.1
-
51
-
-
0025916872
-
Functionality Maps of Binding Sites: A Multiple Copy Simultaneous Search Method
-
Miranker, A.; Karplus, M. Functionality Maps of Binding Sites: A Multiple Copy Simultaneous Search Method. Proteins 1991, 11, 29-34.
-
(1991)
Proteins
, vol.11
, pp. 29-34
-
-
Miranker, A.1
Karplus, M.2
-
52
-
-
0027027467
-
Ludi - Rule-based Automatic Design of New Substituents for Enzyme-Inhibitor Leads
-
Böhm, H.-J. Ludi - Rule-based Automatic Design of New Substituents for Enzyme-Inhibitor Leads. J. Comput.-Aided Mol. Design 1992, 6, 593-606.
-
(1992)
J. Comput.-Aided Mol. Design
, vol.6
, pp. 593-606
-
-
Böhm, H.-J.1
-
53
-
-
0033214412
-
Exhaustive Docking of Molecular Fragments on Protein Binding Sites with Electrostatic Solvation
-
Majeux, N.; Scarsi, M.; Apostolakis, J.; Ehrhardt, C.; Caflisch, A. Exhaustive Docking of Molecular Fragments on Protein Binding Sites with Electrostatic Solvation. Proteins 1999, 37, 88-105.
-
(1999)
Proteins
, vol.37
, pp. 88-105
-
-
Majeux, N.1
Scarsi, M.2
Apostolakis, J.3
Ehrhardt, C.4
Caflisch, A.5
-
54
-
-
0030154893
-
Hammerhead: Fast, Fully Automated Docking of Flexible Ligands to Protein Binding Sites
-
Welch, W.; Ruppert, J.; Jain, A. N. Hammerhead: Fast, Fully Automated Docking of Flexible Ligands to Protein Binding Sites. Chem. & Biol. 1996, 3, 449-462.
-
(1996)
Chem. & Biol.
, vol.3
, pp. 449-462
-
-
Welch, W.1
Ruppert, J.2
Jain, A.N.3
-
55
-
-
0036022961
-
Q-fit: A Probabilistic Method for Docking Molecular Fragments by Sampling Low Energy Conformational Space
-
Jackson, R. M. Q-fit: A Probabilistic Method for Docking Molecular Fragments by Sampling Low Energy Conformational Space. J. Comput.-Aided Mol. Design 2002, 16, 43-57.
-
(2002)
J. Comput.-Aided Mol. Design
, vol.16
, pp. 43-57
-
-
Jackson, R.M.1
-
56
-
-
0037434582
-
Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-based Search Engine
-
Jain, A. N.; Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-based Search Engine. J. Med. Chem. 2003, 46, 499-511.
-
(2003)
J. Med. Chem.
, vol.46
, pp. 499-511
-
-
Jain, A.N.1
-
57
-
-
0000681927
-
Pharmacophore-based Molecular Docking
-
Güner O.F. (Ed.), International University Line: La Jolla (CA), USA
-
Thomas IV, B. E.; Joseph-McCarthy, D.; Alvarez, J. C. Pharmacophore-based Molecular Docking. In Güner, O.F. (Ed.), Pharmacophore Perception, Development and Use in Drug Design. International University Line: La Jolla (CA), USA, 2000, pp. 351-367.
-
(2000)
Pharmacophore Perception, Development and Use in Drug Design
, pp. 351-367
-
-
Thomas IV, B.E.1
Joseph-McCarthy, D.2
Alvarez, J.C.3
-
58
-
-
0037402105
-
Pharmacophore-based Molecular Docking to Account for Ligand Flexibility
-
Joseph-McCarthy, D.; Thomas IV, B. E.; Belmarsh, M.; Moustakas, D.; Alvarez, J. C. Pharmacophore-based Molecular Docking to Account for Ligand Flexibility. Proteins 2003, 51, 172-188.
-
(2003)
Proteins
, vol.51
, pp. 172-188
-
-
Joseph-McCarthy, D.1
Thomas IV, B.E.2
Belmarsh, M.3
Moustakas, D.4
Alvarez, J.C.5
-
59
-
-
0034780805
-
Fragment-based Flexible Ligand Docking by Evolutionary Optimization
-
Budin, N.; Majeux, N.; Caflisch, A. Fragment-based Flexible Ligand Docking by Evolutionary Optimization. Biol. Chem. 2001, 382, 1365-1372.
-
(2001)
Biol. Chem.
, vol.382
, pp. 1365-1372
-
-
Budin, N.1
Majeux, N.2
Caflisch, A.3
-
60
-
-
0034632804
-
DoMCoSAR: A Novel Approach for Establishing the Docking Mode that is Consistent with the Structure-Activity Relationship. Application to HIV-1 Protease Inhibitors and VEGF Receptor Tyrosine Kinase Inhibitors
-
Vieth, M.; Cummins, D. J. DoMCoSAR: A Novel Approach for Establishing the Docking Mode that is Consistent with the Structure-Activity Relationship. Application to HIV-1 Protease Inhibitors and VEGF Receptor Tyrosine Kinase Inhibitors. J. Med. Chem. 2000, 43, 3020-3032.
-
(2000)
J. Med. Chem.
, vol.43
, pp. 3020-3032
-
-
Vieth, M.1
Cummins, D.J.2
-
61
-
-
0035865951
-
Design, Docking, and Evaluation of Multiple Libraries against Multiple Targets
-
Lamb, M. L.; Burdick, K. W.; Toba, S.; Young, M. M.; Skillman, A. G.; Zou, X.; Arnold, J. R.; Kuntz, I. D. Design, Docking, and Evaluation of Multiple Libraries against Multiple Targets. Proteins 2001, 42, 296-318.
-
(2001)
Proteins
, vol.42
, pp. 296-318
-
-
Lamb, M.L.1
Burdick, K.W.2
Toba, S.3
Young, M.M.4
Skillman, A.G.5
Zou, X.6
Arnold, J.R.7
Kuntz, I.D.8
-
62
-
-
0034284367
-
Similarity-driven Flexible Ligand Docking
-
Fradera, X; Knegtel, R. M. A.; Mestres, J. Similarity-driven Flexible Ligand Docking. Proteins 2000, 40, 623-636.
-
(2000)
Proteins
, vol.40
, pp. 623-636
-
-
Fradera, X.1
Knegtel, R.M.A.2
Mestres, J.3
-
63
-
-
6244283606
-
Critical Evaluation of Search Algorithms for Automated Molecular Docking and Database Screening
-
Ewing, T.; Kuntz, I. D. Critical Evaluation of Search Algorithms for Automated Molecular Docking and Database Screening. J. Comput. Chem. 1997, 18, 1175-1189.
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 1175-1189
-
-
Ewing, T.1
Kuntz, I.D.2
-
64
-
-
3042566294
-
-
GOLD version 1.2, July
-
GOLD version 1.2 (July 2001): http://www.ccdc.cam.ac.uk/support/prods_doc/gold/GOLDdocn.html
-
(2001)
-
-
-
65
-
-
0034981694
-
Structure Prediction of Protein Complexes by an NMR-based Protein Docking Algorithm
-
Kohlbacher, O.; Burchardt, A.; Moll, A.; Hildebrandt, A.; Bayer, P.; Lenhof, H.-P. Structure Prediction of Protein Complexes by an NMR-based Protein Docking Algorithm. J. Biomol. NMR 2001, 20, 15-21.
-
(2001)
J. Biomol. NMR
, vol.20
, pp. 15-21
-
-
Kohlbacher, O.1
Burchardt, A.2
Moll, A.3
Hildebrandt, A.4
Bayer, P.5
Lenhof, H.-P.6
-
66
-
-
0034808070
-
A Novel Approach for Assessing Macromolecular Complexes Combining Soft-Docking Calculations with NMR Data
-
Morelli, X. J.; Palma, P. N.; Guerlesquin, F.; Rigby, A. C. A Novel Approach for Assessing Macromolecular Complexes Combining Soft-Docking Calculations with NMR Data. Prot. Sci. 2001, 10, 2131-2137.
-
(2001)
Prot. Sci.
, vol.10
, pp. 2131-2137
-
-
Morelli, X.J.1
Palma, P.N.2
Guerlesquin, F.3
Rigby, A.C.4
-
67
-
-
0037442962
-
HADDOCK: A Protein-Protein Docking Approach Based on Biochemical or Biophysical Information
-
Dominguez, C.; Boelens, C.; Bonvin, A. M. J. J. HADDOCK: A Protein-Protein Docking Approach Based on Biochemical or Biophysical Information. J. Am. Chem. Soc. 2003, 125, 1731-1737.
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 1731-1737
-
-
Dominguez, C.1
Boelens, C.2
Bonvin, A.M.J.J.3
-
69
-
-
0035812704
-
Global Efforts in Structural Genomics
-
Stevens, R.C.; Yokoyama, S.; Wilson, I.A. Global Efforts in Structural Genomics. Science 2001, 294, 89-92.
-
(2001)
Science
, vol.294
, pp. 89-92
-
-
Stevens, R.C.1
Yokoyama, S.2
Wilson, I.A.3
-
70
-
-
0037349370
-
Facilities and Methods for the High-Throughput Crystal Structure Analysis of Human Proteins
-
Heinemann, U.; Büssow, K.; Mueller, U.; Umbach, P. Facilities and Methods for the High-Throughput Crystal Structure Analysis of Human Proteins. Acc. Chem. Res. 2003, 36, 157-163.
-
(2003)
Acc. Chem. Res.
, vol.36
, pp. 157-163
-
-
Heinemann, U.1
Büssow, K.2
Mueller, U.3
Umbach, P.4
-
71
-
-
0033168872
-
High-Throughput NMR-based Screening
-
Hajduk, P.J.; Gerfin, T.; Boehlen, J.-M.; Häberli, M.; Marek, D.; Fesik, S.W. High-Throughput NMR-based Screening. J. Med. Chem. 1999, 42, 2315-2317.
-
(1999)
J. Med. Chem.
, vol.42
, pp. 2315-2317
-
-
Hajduk, P.J.1
Gerfin, T.2
Boehlen, J.-M.3
Häberli, M.4
Marek, D.5
Fesik, S.W.6
-
72
-
-
0036051992
-
High-Throughput Crystallography for Lead Discovery in Drug Design
-
Blundell, T.L.; Jhoti, H.; Abell, C. High-Throughput Crystallography for Lead Discovery in Drug Design. Nature Rev. Drug Discov. 2002, 1, 45-54.
-
(2002)
Nature Rev. Drug Discov.
, vol.1
, pp. 45-54
-
-
Blundell, T.L.1
Jhoti, H.2
Abell, C.3
-
73
-
-
0037441549
-
Strategies for Structural Proteomics of Prokaryotes: Quantifying the Advantages of Studying Orthologous Proteins and of Using Both NMR and X-Ray Crystallography Approaches
-
Savchenko, A.; Yee, A.; Khachatryan, A.; Skarina, T.; Evdokimova, E.; Pavlova, M.; Semesi, A.; Northey, J.; Beasley, S.; Lan, N.; Das, R.; Gerstein, M.; Arrowmith, C.H.; Edwards, A.M. Strategies for Structural Proteomics of Prokaryotes: Quantifying the Advantages of Studying Orthologous Proteins and of Using Both NMR and X-Ray Crystallography Approaches. Proteins 2003, 50, 392-399.
-
(2003)
Proteins
, vol.50
, pp. 392-399
-
-
Savchenko, A.1
Yee, A.2
Khachatryan, A.3
Skarina, T.4
Evdokimova, E.5
Pavlova, M.6
Semesi, A.7
Northey, J.8
Beasley, S.9
Lan, N.10
Das, R.11
Gerstein, M.12
Arrowmith, C.H.13
Edwards, A.M.14
-
74
-
-
0037048588
-
Structure-based Screening as Applied to Human FABP4: A Highly Efficient Alternative to HTS for Hit Generation
-
Van Dongen, M.J.P.; Uppenberg, J.; Svensson, S.; Lundbäck, T.; Åkerud, T.; Wikström, M.; Schultz, J. Structure-based Screening as Applied to Human FABP4: A Highly Efficient Alternative to HTS for Hit Generation. J. Am. Chem. Soc. 2002, 124, 11874-11880.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 11874-11880
-
-
Van Dongen, M.J.P.1
Uppenberg, J.2
Svensson, S.3
Lundbäck, T.4
Åkerud, T.5
Wikström, M.6
Schultz, J.7
|