-
1
-
-
0001462919
-
Three-dimensional pharmacophoric pattern searching
-
Gund, P. Three-dimensional Pharmacophoric Pattern Searching. Prog. Mol. Subcell. Biol. 1977, 5, 117-143.
-
(1977)
Prog. Mol. Subcell. Biol.
, vol.5
, pp. 117-143
-
-
Gund, P.1
-
3
-
-
0141882047
-
History and evolution of the pharmacophore model concept in computer-aided drug design
-
Güner, O. F. History and evolution of the pharmacophore model concept in computer-aided drug design. Curr. Top. Med. Chem. 2002, 2, 1321-1332.
-
(2002)
Curr. Top. Med. Chem.
, vol.2
, pp. 1321-1332
-
-
Güner, O.F.1
-
4
-
-
0347755449
-
Predicting molecular interactions in silico: 1. A guide to pharmacophore identification and its applications to drug design
-
Dror, O.; Shulman-Peleg, A.; Nussinov R.; Wolfson, H. J. Predicting Molecular Interactions in silico: 1. A Guide to Pharmacophore Identification and its Applications to Drug Design. Curr. Med. Chem. 2004, 11, 71-90.
-
(2004)
Curr. Med. Chem.
, vol.11
, pp. 71-90
-
-
Dror, O.1
Shulman-Peleg, A.2
Nussinov, R.3
Wolfson, H.J.4
-
5
-
-
0027548454
-
A fast new approach to pharmacophore model mapping and its application to dopaminergic and benzodiazepine agonists
-
Martin, Y. C.; Bures, M. G.; Danaher, E. A.; DeLazzer, J.; Lico, I.; Pavlik, P. A. A fast new approach to pharmacophore model mapping and its application to dopaminergic and benzodiazepine agonists. J. Comput.-Aided Mol. Des. 1993, 7, 83-102.
-
(1993)
J. Comput.-aided Mol. Des.
, vol.7
, pp. 83-102
-
-
Martin, Y.C.1
Bures, M.G.2
Danaher, E.A.3
Delazzer, J.4
Lico, I.5
Pavlik, P.A.6
-
6
-
-
0030137662
-
Identification of common functional configurations among molecules
-
Barnum, D.; Greene, J.; Smellie, A.; Sprague, P. Identification of common functional configurations among molecules. J. Chem. Inf. Comput. Sci. 1996, 36, 563-571.
-
(1996)
J. Chem. Inf. Comput. Sci.
, vol.36
, pp. 563-571
-
-
Barnum, D.1
Greene, J.2
Smellie, A.3
Sprague, P.4
-
7
-
-
0028550028
-
Chemical function queries for 3D database search
-
Greene, J.; Kahn, S.; Savoj, H.; Sprague, P.; Teig, S. Chemical Function Queries for 3D Database Search. J. Chem. Inf. Comput. Sci. 1994, 34, 1297-1308.
-
(1994)
J. Chem. Inf. Comput. Sci.
, vol.34
, pp. 1297-1308
-
-
Greene, J.1
Kahn, S.2
Savoj, H.3
Sprague, P.4
Teig, S.5
-
8
-
-
84986522856
-
Poling: Promoting conformational variation
-
Smellie, A.; Teig, S. L.; Towbin, P. Poling: Promoting conformational variation. J. Comput. Chem. 1995, 16, 171-187.
-
(1995)
J. Comput. Chem.
, vol.16
, pp. 171-187
-
-
Smellie, A.1
Teig, S.L.2
Towbin, P.3
-
9
-
-
0029444383
-
A genetic algorithm for flexible molecular overlay and pharmacophore model elucidation
-
Jones, G.; Willett, P.; Glen, R. C. A genetic algorithm for flexible molecular overlay and pharmacophore model elucidation. J. Comput.-Aided Mol. Des. 1995, 9, 532-549.
-
(1995)
J. Comput.-aided Mol. Des.
, vol.9
, pp. 532-549
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
-
10
-
-
0041488802
-
Pharmacophore discovery -Lessons learned
-
John H. V. D. Pharmacophore discovery -Lessons learned. Curr. Pharm. Des. 2003, 9, 1649-1664.
-
(2003)
Curr. Pharm. Des.
, vol.9
, pp. 1649-1664
-
-
John, H.V.D.1
-
11
-
-
0036706746
-
A comparison of the pharmacophore model identification programs: Catalyst, DISCO and GASP
-
Patel, Y.; Gillet, V. J.; Bravi, G.; Leach, A. R. A comparison of the pharmacophore model identification programs: Catalyst, DISCO and GASP. J. Comput. -Aided Mol. Des. 2002, 16, 653-681.
-
(2002)
J. Comput. -aided Mol. Des.
, vol.16
, pp. 653-681
-
-
Patel, Y.1
Gillet, V.J.2
Bravi, G.3
Leach, A.R.4
-
13
-
-
0021871375
-
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
-
Goodford, P. J. 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.J.1
-
14
-
-
0024566942
-
New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure
-
Boobbyer, D. N.; Goodford, P. J.; McWhinnie, P. M.; Wade, R. C. New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure. J. Med. Chem. 1989, 32, 1083-1094.
-
(1989)
J. Med. Chem.
, vol.32
, pp. 1083-1094
-
-
Boobbyer, D.N.1
Goodford, P.J.2
McWhinnie, P.M.3
Wade, R.C.4
-
15
-
-
0036406643
-
A new method to detect related function among proteins independent of sequence and fold homology
-
Schmitt, S.; Kuhn, D.; Klebe, G. A new method to detect related function among proteins independent of sequence and fold homology. J. Mol Biol. 2002, 323, 387-406.
-
(2002)
J. Mol Biol.
, vol.323
, pp. 387-406
-
-
Schmitt, S.1
Kuhn, D.2
Klebe, G.3
-
16
-
-
0141482410
-
Common structural cliques: A tool for protein structure and function analysis
-
Mariusz M.; SaǍndor S.; Krzysztof A. O. Common Structural Cliques: a tool for protein structure and function analysis. Protein Eng. 2003, 16, 543-552.
-
(2003)
Protein Eng.
, vol.16
, pp. 543-552
-
-
Mariusz, M.1
Saǎndor, S.2
Krzysztof, A.O.3
-
17
-
-
0026813925
-
The computer program LUDI: A new method for the de novo design of enzyme inhibitors
-
Bohm, H. J. The computer program LUDI: a new method for the de novo design of enzyme inhibitors. J. Comput.-Aided Mol. Des. 1992, 6, 61-78.
-
(1992)
J. Comput.-aided Mol. Des.
, vol.6
, pp. 61-78
-
-
Bohm, H.J.1
-
18
-
-
0027027467
-
LUDI: Rule-based automatic design of new substituents for enzyme inhibitor leads
-
Bohm, H. J. LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads. J. Comput.-Aided Mol. Des. 1992, 6, 593-606.
-
(1992)
J. Comput.-aided Mol. Des.
, vol.6
, pp. 593-606
-
-
Bohm, H.J.1
-
19
-
-
0029242576
-
PRO_LIGAND: An approach to de novo molecular design. 1. Application to the design of organic moleculars
-
Clark, D. E.; Frenkel, D. F.; Levy, S. A.; Li, J.; Murray C. W.; Robson, B.; Waszkowycz, B.; Westhead, D. R. PRO_LIGAND: An approach to de novo molecular design. 1. Application to the design of organic moleculars. J. Comput.-Aided Mol. Des. 1995, 9, 13-32.
-
(1995)
J. Comput.-aided Mol. Des.
, vol.9
, pp. 13-32
-
-
Clark, D.E.1
Frenkel, D.F.2
Levy, S.A.3
Li, J.4
Murray, C.W.5
Robson, B.6
Waszkowycz, B.7
Westhead, D.R.8
-
20
-
-
0030253210
-
Activesite-directed 3D database searching: Pharmacophore extraction and validation of hits
-
Clark, D. E.; Westhead, D. R.; Sykes, R. A.; Murray, C. W. Activesite-directed 3D database searching: Pharmacophore extraction and validation of hits. J. Comput.-Aided Mol. Des. 1996, 10, 397-416.
-
(1996)
J. Comput.-aided Mol. Des.
, vol.10
, pp. 397-416
-
-
Clark, D.E.1
Westhead, D.R.2
Sykes, R.A.3
Murray, C.W.4
-
21
-
-
0035002051
-
Structure-based focusing using pharmacophore models derived from the active site of 17beta-hydroxysteroid dehydrogenase
-
Hoffren, A. M.; Murray, C. M.; Hoffmann, R. D. Structure-based focusing using pharmacophore models derived from the active site of 17beta-hydroxysteroid dehydrogenase. Curr. Pharm. Des. 2001, 7, 547-566.
-
(2001)
Curr. Pharm. Des.
, vol.7
, pp. 547-566
-
-
Hoffren, A.M.1
Murray, C.M.2
Hoffmann, R.D.3
-
22
-
-
0035974531
-
Application of structure-based focusing to the estrogen receptor
-
Kirchhoff, P. D.; Brown, R.; Kahn, S.; Waldman, M.; Venkatachalam, C. M. Application of Structure-Based Focusing to the Estrogen Receptor. J. Comput. Chem. 2001, 22, 993-1003.
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 993-1003
-
-
Kirchhoff, P.D.1
Brown, R.2
Kahn, S.3
Waldman, M.4
Venkatachalam, C.M.5
-
23
-
-
0000217414
-
LigBuilder: A multi-purpose program for structure-based drug design
-
Wang, R. X.; Gao, Y.; Lai, L. H. LigBuilder: a multi-purpose program for structure-based drug design. J. Mol. Model. 2000, 6, 498-516.
-
(2000)
J. Mol. Model.
, vol.6
, pp. 498-516
-
-
Wang, R.X.1
Gao, Y.2
Lai, L.H.3
-
24
-
-
0001704085
-
Score: A new empirical method for estimating the binding affinity of a protein -ligand complex
-
Wang, R. X.; Liu, L.; Lai, L. H.; Tang, Y. Q. Score: A New Empirical Method for Estimating the Binding Affinity of a Protein -Ligand Complex. J. Mol. Model. 1998, 4, 379-394.
-
(1998)
J. Mol. Model.
, vol.4
, pp. 379-394
-
-
Wang, R.X.1
Liu, L.2
Lai, L.H.3
Tang, Y.Q.4
-
25
-
-
0035966871
-
Detailed analysis of scoring functions for virtual screening
-
Stahl, M.; Rarey, M. Detailed analysis of scoring functions for virtual screening. J. Med. Chem. 2001, 44, 1035-1042.
-
(2001)
J. Med. Chem.
, vol.44
, pp. 1035-1042
-
-
Stahl, M.1
Rarey, M.2
-
26
-
-
0037763817
-
Comparative Evaluation of 11 scoring functions for molecular docking
-
Wang, R. X.; Lu, Y. P.; Wang, S. M. Comparative Evaluation of 11 scoring functions for molecular docking. J. Med. Chem. 2003, 46, 2287-2303.
-
(2003)
J. Med. Chem.
, vol.46
, pp. 2287-2303
-
-
Wang, R.X.1
Lu, Y.P.2
Wang, S.M.3
-
27
-
-
0035011980
-
Protein ligand docking based on empirical method for binding affinity estimation
-
Tao, P.; Lai, L. H. Protein ligand docking based on empirical method for binding affinity estimation. J. Comput.-Aided Mol. Des. 2001, 5, 429-446.
-
(2001)
J. Comput.-aided Mol. Des.
, vol.5
, pp. 429-446
-
-
Tao, P.1
Lai, L.H.2
-
28
-
-
0032214649
-
Databases for protein-ligand complexes
-
Hendlich, M. Databases for Protein-Ligand Complexes. Acta Crystallogr. 1998, 54, 1178-1182.
-
(1998)
Acta Crystallogr.
, vol.54
, pp. 1178-1182
-
-
Hendlich, M.1
-
29
-
-
20444422149
-
The PDBbind database: Methodologies and updates
-
Wang, R.; Fang, X.; Lu, Y.; Yang, C.-Y.; Wang, S. The PDBbind Database: Methodologies and updates. J. Med. Chem. 2005, 48, 4111-4119.
-
(2005)
J. Med. Chem.
, vol.48
, pp. 4111-4119
-
-
Wang, R.1
Fang, X.2
Lu, Y.3
Yang, C.-Y.4
Wang, S.5
-
30
-
-
2542530042
-
The PDBbind Database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures
-
Wang, R.; Fang, X.; Lu, Y.; Wang, S. The PDBbind Database: Collection of Binding Affinities for Protein-Ligand Complexes with Known Three-Dimensional Structures. J. Med. Chem. 2004, 47, 2977-2980.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 2977-2980
-
-
Wang, R.1
Fang, X.2
Lu, Y.3
Wang, S.4
-
31
-
-
0037666888
-
Implications of protein flexibility for drug discovery
-
Teague, S. J. Implications of protein flexibility for drug discovery. Nat. Rev. Drug Discovery 2003, 2, 527-541.
-
(2003)
Nat. Rev. Drug Discovery
, vol.2
, pp. 527-541
-
-
Teague, S.J.1
-
32
-
-
0347361642
-
Lessons in molecular recognition: The effects of ligand and protein flexibility on molecular docking accuracy
-
Erickson, J. A.; Jalaie, M.; Robertson, D. H.; Lewis, R. A.; Vieth, M. Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy. J. Med. Chem. 2004, 47, 45-55.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 45-55
-
-
Erickson, J.A.1
Jalaie, M.2
Robertson, D.H.3
Lewis, R.A.4
Vieth, M.5
-
33
-
-
0036019065
-
Protein flexibility is an important component of structure-based drug discovery
-
Carlson, H. A. Protein flexibility is an important component of structure-based drug discovery. Curr. Pharm. Des. 2002, 8, 1571-1578.
-
(2002)
Curr. Pharm. Des.
, vol.8
, pp. 1571-1578
-
-
Carlson, H.A.1
-
34
-
-
0346022974
-
Understanding protein-ligand interactions: The price of protein flexibility
-
Rauh, D.; Klebe, G.; Stubbs, M. T. Understanding protein-ligand interactions: the price of protein flexibility. J. Mol. Biol. 2004, 335, 1325-1341.
-
(2004)
J. Mol. Biol.
, vol.335
, pp. 1325-1341
-
-
Rauh, D.1
Klebe, G.2
Stubbs, M.T.3
-
35
-
-
0033974667
-
Accommodating protein flexibility in computational drug design
-
Carlson, H. A.; McCammon, J. A. Accommodating protein flexibility in computational drug design. Mol. Pharmacol. 2000, 57, 213-218.
-
(2000)
Mol. Pharmacol.
, vol.57
, pp. 213-218
-
-
Carlson, H.A.1
McCammon, J.A.2
-
36
-
-
0036680063
-
Protein flexibility and drug design: How to hit a moving target
-
Carlson, H. A. Protein flexibility and drug design: how to hit a moving target. Curr. Opin. Chem. Biol. 2002, 6, 447-452.
-
(2002)
Curr. Opin. Chem. Biol.
, vol.6
, pp. 447-452
-
-
Carlson, H.A.1
-
38
-
-
84986432941
-
Automated docking with grid-based energy evaluation
-
Meng E. C.; Shoichet B. K.; Kuntz I. D. Automated docking with grid-based energy evaluation. J. Comput. Chem. 1992, 13, 505-524.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 505-524
-
-
Meng, E.C.1
Shoichet, B.K.2
Kuntz, I.D.3
-
40
-
-
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, 723-732.
-
(1993)
Protein Eng.
, vol.6
, pp. 723-732
-
-
Shoichet, B.K.1
Kuntz, I.D.2
-
41
-
-
0028057975
-
Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors
-
Lam, P. Y.; Jadhav, P. K.; Eyermann, C. J.; Hodge, C. N.; Ru, Y.; Bacheler, L. T.; Meek, J. L.; Otto, M. J.; Rayner, M. M.; Wong, Y. N. Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors. Science 1994, 263, 380-384.
-
(1994)
Science
, vol.263
, pp. 380-384
-
-
Lam, P.Y.1
Jadhav, P.K.2
Eyermann, C.J.3
Hodge, C.N.4
Ru, Y.5
Bacheler, L.T.6
Meek, J.L.7
Otto, M.J.8
Rayner, M.M.9
Wong, Y.N.10
-
42
-
-
0028922586
-
LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
-
Wallace, A. C.; Laskowski, R. A.; Thornton J. M. LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 1995, 8, 127-134.
-
(1995)
Protein Eng.
, vol.8
, pp. 127-134
-
-
Wallace, A.C.1
Laskowski, R.A.2
Thornton, J.M.3
|