-
1
-
-
1442293369
-
Current state and perspectives of 3D-QSAR
-
Akamatsu, M. Current state and perspectives of 3D-QSAR. Curr. Top. Med. Chem. 2002, 12, 1381-1394
-
(2002)
Curr. Top. Med. Chem.
, vol.12
, pp. 1381-1394
-
-
Akamatsu, M.1
-
2
-
-
0023751431
-
Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins
-
Cramer, R. D., III; Patterson, D. E.; Bunce, J. D. Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc. 1988, 110, 5959-5967.
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 5959-5967
-
-
Cramer III, R.D.1
Patterson, D.E.2
Bunce, J.D.3
-
3
-
-
0023677388
-
Three-dimensional structure-activity relationships
-
Marshall, G. R.; Cramer, R. D., III. Three-dimensional structure-activity relationships. Trends Pharmacol. Sci. 1988, 9, 285-289.
-
(1988)
Trends Pharmacol. Sci.
, vol.9
, pp. 285-289
-
-
Marshall, G.R.1
Cramer III, R.D.2
-
4
-
-
0002100415
-
-
Waterbeemd, H., Ed.; VCH: Weinheim, Germany
-
Clementi, S.; Wold, S. In Chemometric Methods in Molecular Design; Waterbeemd, H., Ed.; VCH: Weinheim, Germany, 1995; pp 319-338.
-
(1995)
Chemometric Methods in Molecular Design
, pp. 319-338
-
-
Clementi, S.1
Wold, S.2
-
5
-
-
0000295654
-
-
Waterbeemd, H., Ed.; VCH: Weinheim, Germany
-
Wold, S.; Eriksson, L. In Chemometric Methods in Molecular Design; Waterbeemd, H., Ed.; VCH: Weinheim, Germany, 1995; pp 309-318.
-
(1995)
Chemometric Methods in Molecular Design
, pp. 309-318
-
-
Wold, S.1
Eriksson, L.2
-
6
-
-
0028046665
-
Variable selection in QSAR studies. I. An evolutionary algorithm
-
Kubinyi, H. Variable selection in QSAR studies. I. An evolutionary algorithm. Quant. Struct.-Act. Relat. 1994, 13, 285-294.
-
(1994)
Quant. Struct.-Act. Relat.
, vol.13
, pp. 285-294
-
-
Kubinyi, H.1
-
8
-
-
0000295654
-
-
Water-beemd, H., Ed.; VCH: Weinheim, Germany
-
Wold, S. In Chemometric Methods in Molecular Design; Water-beemd, H., Ed.; VCH: Weinheim, Germany, 1995; pp 195-218.
-
(1995)
Chemometric Methods in Molecular Design
, pp. 195-218
-
-
Wold, S.1
-
9
-
-
84987100711
-
Crossvalidation, bootstrapping and PLS compared with multiple linear regression in conventional QSAR studies
-
Cramer, R. D., III; Bunce, J. D.; Patterson, D. E. Crossvalidation, bootstrapping and PLS compared with multiple linear regression in conventional QSAR studies. Quant. Struct.-Act. Relat. 1988, 7, 18-28.
-
(1988)
Quant. Struct.-Act. Relat.
, vol.7
, pp. 18-28
-
-
Cramer III, R.D.1
Bunce, J.D.2
Patterson, D.E.3
-
10
-
-
0035157466
-
3D-quantitative structure activity relationships of biphenyl carboxylic acid MMP-3 inhibitors: Exploring automated docking as alignment method
-
Muegge, I.; Podlogar, B. L. 3D-quantitative structure activity relationships of biphenyl carboxylic acid MMP-3 inhibitors: exploring automated docking as alignment method. Quant. Struct.-Act. Relat. 2001, 20, 215-222.
-
(2001)
Quant. Struct.-Act. Relat.
, vol.20
, pp. 215-222
-
-
Muegge, I.1
Podlogar, B.L.2
-
11
-
-
0032812604
-
Automated docking of 82 N-benzylpiperidine derivatives to mouse acetylcholinesterase and comparative molecular field analysis with "natural" alignment
-
Bernard, P.; Kireev, D. B.; Chrétien, J. R.; Fortier, P. L.; Coppet, L. Automated docking of 82 N-benzylpiperidine derivatives to mouse acetylcholinesterase and comparative molecular field analysis with "natural" alignment. J. Comput.-Aided Mol. Des. 1999, 13, 355-371.
-
(1999)
J. Comput.-Aided Mol. Des.
, vol.13
, pp. 355-371
-
-
Bernard, P.1
Kireev, D.B.2
Chrétien, J.R.3
Fortier, P.L.4
Coppet, L.5
-
12
-
-
0000261607
-
Structure-based alignment and comparative molecular field analysis of acetyl-cholinesterase inhibitors
-
Cho, S. J.; Garsia, M. L.; Bier, J.; Tropsha, A. Structure-based alignment and comparative molecular field analysis of acetyl-cholinesterase inhibitors. J. Med. Chem. 1996, 39, 5064-5071.
-
(1996)
J. Med. Chem.
, vol.39
, pp. 5064-5071
-
-
Cho, S.J.1
Garsia, M.L.2
Bier, J.3
Tropsha, A.4
-
13
-
-
0032015246
-
Evaluation of proposed modes of binding of (2S)-2- [4-[[(3S)-1- acetimidoyl-3-pyrrolidinyl]-oxy]phenyl]-3-(7-am idino-2-naphthyl)propanoic acid hydrochloride and some analogues to factor Xa using a comparative molecular field analysis
-
Vaz, R. J.; McLean, L. R.; Pelton, J. T. Evaluation of proposed modes of binding of (2S)-2- [4-[[(3S)-1-acetimidoyl-3-pyrrolidinyl]-oxy]phenyl]-3-(7-am idino-2-naphthyl)propanoic acid hydrochloride and some analogues to factor Xa using a comparative molecular field analysis. J. Comput.-Aided Mol. Des. 1998, 12, 99-110.
-
(1998)
J. Comput.-Aided Mol. Des.
, vol.12
, pp. 99-110
-
-
Vaz, R.J.1
McLean, L.R.2
Pelton, J.T.3
-
14
-
-
0034050042
-
3D-QSAR methods on the basis of ligand-receptor complexes. Application of COMBINE and GRID/GOLPE methodologies to a series of CYP1A2 ligands
-
Lozano, J. J.; Pastor, M.; Cruciani, G.; Gaedt, K.; Centeno, N. B.; Gago, F.; Sanz, F. 3D-QSAR methods on the basis of ligand-receptor complexes. Application of COMBINE and GRID/GOLPE methodologies to a series of CYP1A2 ligands. J. Comput.-Aided Mol. Des. 2000, 13, 341-353.
-
(2000)
J. Comput.-Aided Mol. Des.
, vol.13
, pp. 341-353
-
-
Lozano, J.J.1
Pastor, M.2
Cruciani, G.3
Gaedt, K.4
Centeno, N.B.5
Gago, F.6
Sanz, F.7
-
15
-
-
0035111276
-
A molecular modeling and 3D QSAR study of a large series of indole inhibitors of human nonpancreatic secretory phospholipase A2
-
Bernard, P.; Pintore, M.; Berthon, J.-Y.; Chretien, J. R. A molecular modeling and 3D QSAR study of a large series of indole inhibitors of human nonpancreatic secretory phospholipase A2. Eur. J. Med. Chem. 2001, 36, 1-19.
-
(2001)
Eur. J. Med. Chem.
, vol.36
, pp. 1-19
-
-
Bernard, P.1
Pintore, M.2
Berthon, J.-Y.3
Chretien, J.R.4
-
16
-
-
0035118774
-
Protein-based alignment in 3D QSAR of 26 indole inhibitors of human pancreatic phospholipase A2
-
Pintore, M.; Bernard, P.; Berthon, J.-Y.; Chretien, J. R. Protein-based alignment in 3D QSAR of 26 indole inhibitors of human pancreatic phospholipase A2. Eur. J. Med. Chem. 2001, 36, 21-30.
-
(2001)
Eur. J. Med. Chem.
, vol.36
, pp. 21-30
-
-
Pintore, M.1
Bernard, P.2
Berthon, J.-Y.3
Chretien, J.R.4
-
17
-
-
0034011785
-
Validation of protein-based alignment in 3D quantitative structure-activity relationships with CoMFA models
-
Golbraikh, A.; Bernard, P.; Chretien, J. R. Validation of protein-based alignment in 3D quantitative structure-activity relationships with CoMFA models. Eur. J. Med. Chem. 2000, 35, 123-136.
-
(2000)
Eur. J. Med. Chem.
, vol.35
, pp. 123-136
-
-
Golbraikh, A.1
Bernard, P.2
Chretien, J.R.3
-
18
-
-
0242577782
-
CoMFA and docking study of novel estrogen receptor subtype selective ligands
-
Wolohan, P.; Reichert, D. E. CoMFA and docking study of novel estrogen receptor subtype selective ligands. J. Comput.-Aided Mol. Des. 2003, 17, 313-328.
-
(2003)
J. Comput.-Aided Mol. Des.
, vol.17
, pp. 313-328
-
-
Wolohan, P.1
Reichert, D.E.2
-
19
-
-
0037837211
-
Development of biologically active compounds by combining 3D QSAR and structure-based design methods
-
Sippl, W. Development of biologically active compounds by combining 3D QSAR and structure-based design methods. J. Comput.-Aided Mol. Des. 2002, 16, 825-830.
-
(2002)
J. Comput.-Aided Mol. Des.
, vol.16
, pp. 825-830
-
-
Sippl, W.1
-
20
-
-
12844262293
-
Molecular docking and 3D-QSAR studies of Yersinia protein tyrosine phosphatase YopH inhibitors
-
Hu, X.; Stebbins, C. E. Molecular docking and 3D-QSAR studies of Yersinia protein tyrosine phosphatase YopH inhibitors. Bioorg. Med. Chem. 2005, 13, 1101-1109.
-
(2005)
Bioorg. Med. Chem.
, vol.13
, pp. 1101-1109
-
-
Hu, X.1
Stebbins, C.E.2
-
21
-
-
19944429228
-
Combined target-based and ligand-based drug design approach as a tool to define a novel 3D-pharmaco-phore model of human A3 adenosine receptor antagonists: Pyrazolo[4,3-e] 1,2,4-triazolo[1,5-c] pyrimidine derivatives as a key study
-
Moro, S.; Braiuca, P.; Deflorian, F.; Ferrari, C.; Pastorin, G.; Cacciari, B.; Baraldi, P. G.; Varani, K.; Borea, P. A.; Spalluto, G. Combined target-based and ligand-based drug design approach as a tool to define a novel 3D-pharmaco-phore model of human A3 adenosine receptor antagonists: pyrazolo[4,3-e] 1,2,4-triazolo[1,5-c] pyrimidine derivatives as a key study. J. Med. Chem. 2005, 48, 152-162.
-
(2005)
J. Med. Chem.
, vol.48
, pp. 152-162
-
-
Moro, S.1
Braiuca, P.2
Deflorian, F.3
Ferrari, C.4
Pastorin, G.5
Cacciari, B.6
Baraldi, P.G.7
Varani, K.8
Borea, P.A.9
Spalluto, G.10
-
22
-
-
7744247282
-
A CoMFA study of COX-2 inhibitors with receptor based alignment
-
Datar P. A.; Coutinho, E. C. A CoMFA study of COX-2 inhibitors with receptor based alignment. J. Mol. Graphics Modell. 2004, 23, 239-251.
-
(2004)
J. Mol. Graphics Modell.
, vol.23
, pp. 239-251
-
-
Datar, P.A.1
Coutinho, E.C.2
-
23
-
-
84956774523
-
Protein-Ligand docking
-
Morris, G. M.; Olson, A. J.; Goodsell, D. S. Protein-Ligand docking. Methods Princ. Med. Chem. 2000, 8, 31-48.
-
(2000)
Methods Princ. Med. Chem.
, vol.8
, pp. 31-48
-
-
Morris, G.M.1
Olson, A.J.2
Goodsell, D.S.3
-
25
-
-
0001679526
-
Assessing search strategies for flexible docking
-
Vieth, M.; Hirst, J. D.; Dominy, B. N.; Daigler, H.; Brooks, C. L., III. Assessing search strategies for flexible docking. J. Comput. Chem. 1998, 19, 1623-1631.
-
(1998)
J. Comput. Chem.
, vol.19
, pp. 1623-1631
-
-
Vieth, M.1
Hirst, J.D.2
Dominy, B.N.3
Daigler, H.4
Brooks III, C.L.5
-
26
-
-
0031058541
-
The statistical-thermodynamic basis for computation of binding affinities: A critical review
-
Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys. J. 1997, 72, 1047-1069.
-
(1997)
Biophys. J.
, vol.72
, pp. 1047-1069
-
-
Gilson, M.K.1
Given, J.A.2
Bush, B.L.3
McCammon, J.A.4
-
27
-
-
0032711930
-
Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems
-
Monard, G.; Merz, K. M., Jr. Combined Quantum Mechanical/Molecular Mechanical Methodologies Applied to Biomolecular Systems. Acc. Chem. Res. 1999, 32, 904-911.
-
(1999)
Acc. Chem. Res.
, vol.32
, pp. 904-911
-
-
Monard, G.1
Merz Jr., K.M.2
-
28
-
-
1642540577
-
Evaluation of docking performance: Comparative data on docking algorithms
-
Kontoyianni, M.; McClellan, L. M.; Sokol, G. S. Evaluation of Docking Performance: Comparative Data on Docking Algorithms. J. Med. Chem. 2004, 47, 558-565.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 558-565
-
-
Kontoyianni, M.1
McClellan, L.M.2
Sokol, G.S.3
-
29
-
-
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
-
30
-
-
0035025191
-
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
-
Ewing, T. J. A.; Makino, S.; Skillman, A. G.; Kuntz, I. D. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases. J. Comput. Aided Mol. Des. 2001, 15, 411-428.
-
(2001)
J. Comput. Aided Mol. Des.
, vol.15
, pp. 411-428
-
-
Ewing, T.J.A.1
Makino, S.2
Skillman, A.G.3
Kuntz, I.D.4
-
31
-
-
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
-
32
-
-
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
-
33
-
-
12144289984
-
Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment docking accuracy
-
Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment docking accuracy. J. Med. Chem. 2004, 47, 1739-1749.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 1739-1749
-
-
Friesner, R.A.1
Banks, J.L.2
Murphy, R.B.3
Halgren, T.A.4
Klicic, J.J.5
Mainz, D.T.6
Repasky, M.P.7
Knoll, E.H.8
Shelley, M.9
Perry, J.K.10
Shaw, D.E.11
Francis, P.12
Shenkin, P.S.13
-
34
-
-
0037212102
-
LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites
-
Venkatachalam, C. M.; Jiang, X.; Oldfield, T.; Waldman, M. LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J. Mol. Graphics Modell. 2003, 21, 289-307.
-
(2003)
J. Mol. Graphics Modell.
, vol.21
, pp. 289-307
-
-
Venkatachalam, C.M.1
Jiang, X.2
Oldfield, T.3
Waldman, M.4
-
35
-
-
0034649618
-
Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations
-
Bissantz, C.; Folkers, G.; Rognan, D. Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J. Med. Chem. 2000, 43, 4759-4767.
-
(2000)
J. Med. Chem.
, vol.43
, pp. 4759-4767
-
-
Bissantz, C.1
Folkers, G.2
Rognan, D.3
-
36
-
-
0037763817
-
Comparative evaluation of 11 scoring functions for molecular docking
-
Wang, R.; Lu, Y.; Wang, S. 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.1
Lu, Y.2
Wang, S.3
-
37
-
-
2942720960
-
Impact of scoring functions on enrichment in docking-based virtual screening: An application study on renin inhibitors
-
Krovat, E. M.; Langer, T. Impact of Scoring Functions on Enrichment in Docking- Based Virtual Screening: An Application Study on Renin Inhibitors. J. Chem. Inf. Comput. Sci. 2004, 44, 1123-1129.
-
(2004)
J. Chem. Inf. Comput. Sci.
, vol.44
, pp. 1123-1129
-
-
Krovat, E.M.1
Langer, T.2
-
38
-
-
0031226772
-
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
-
Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J. Comput.-Aided Mol. Des. 1997, 11, 425-445.
-
(1997)
J. Comput.-Aided Mol. Des.
, vol.11
, pp. 425-445
-
-
Eldridge, M.D.1
Murray, C.W.2
Auton, T.R.3
Paolini, G.V.4
Mee, R.P.5
-
39
-
-
0029294584
-
Molecular recognition of the inhibitor AG-1343 by HIV-1 Protease: Conformationally flexible docking by evolutionary programming
-
Gehlhaar, D. K.; Verkhivker, G. M.; Rejto, P. A.; Sherman, C. J.; Fogel, D. B.; Fogel, L. J.; Freer, S. T. Molecular recognition of the inhibitor AG-1343 by HIV-1 Protease: Conformationally flexible docking by evolutionary programming. Chem. Biol. 1995, 2, 317-324.
-
(1995)
Chem. Biol.
, vol.2
, pp. 317-324
-
-
Gehlhaar, D.K.1
Verkhivker, G.M.2
Rejto, P.A.3
Sherman, C.J.4
Fogel, D.B.5
Fogel, L.J.6
Freer, S.T.7
-
40
-
-
0039012103
-
-
Parrill, L., Reddy, M. R., Eds.; American Chemical Society: Washington, DC
-
Gehlhaar, D. K.; Bouzida, D.; Rejto, P. A. In Rational Drug Design: Novel Methodology and Practical Applications; Parrill, L., Reddy, M. R., Eds.; American Chemical Society: Washington, DC, 1999; pp 292-311.
-
(1999)
Rational Drug Design: Novel Methodology and Practical Applications
, pp. 292-311
-
-
Gehlhaar, D.K.1
Bouzida, D.2
Rejto, P.A.3
-
41
-
-
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. Des. 1994, 8, 243-256.
-
(1994)
J. Comput.-Aided Mol. Des.
, vol.8
, pp. 243-256
-
-
Böhm, H.J.1
-
42
-
-
0032112137
-
Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs
-
Böhm, H. J. Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs. J. Comput.-Aided Mol. Des. 1998, 12, 309-323.
-
(1998)
J. Comput.-Aided Mol. Des.
, vol.12
, pp. 309-323
-
-
Böhm, H.J.1
-
43
-
-
0001704085
-
SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex
-
Wang, R.; Gao, Y.; Lai, L. 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.1
Gao, Y.2
Lai, L.3
-
44
-
-
0036022960
-
Further development and validation of empirical scoring functions for structure-based binding validation affinity prediction
-
Wang, R.; Lai, L.; Wang, S. Further development and validation of empirical scoring functions for structure-based binding validation affinity prediction. J. Comput.-Aided Mol. Des. 2002, 16, 11-26.
-
(2002)
J. Comput.-Aided Mol. Des.
, vol.16
, pp. 11-26
-
-
Wang, R.1
Lai, L.2
Wang, S.3
-
45
-
-
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
-
46
-
-
0033673508
-
A knowledge-based scoring function for protein-ligand interactions: Probing the reference state
-
Muegge, I. A knowledge-based scoring function for protein-ligand interactions: Probing the reference state. Perspect. Drug Discovery Des. 2000, 20, 99-114.
-
(2000)
Perspect. Drug Discovery Des.
, vol.20
, pp. 99-114
-
-
Muegge, I.1
-
47
-
-
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
-
48
-
-
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
-
49
-
-
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. Med. Chem. 2002, 45, 2770-2780.
-
(2002)
J. Med. Chem.
, vol.45
, pp. 2770-2780
-
-
Ishchenko, A.V.1
Shakhnovich, E.I.2
-
50
-
-
0032993815
-
Scoring functions: A view from the bench
-
Tame, J. R. H. Scoring functions: a view from the bench. J. Comput.-Aided Mol. Des. 1999, 13, 99-108.
-
(1999)
J. Comput.-Aided Mol. Des.
, vol.13
, pp. 99-108
-
-
Tame, J.R.H.1
-
51
-
-
7044239742
-
Free energy calculations: Applications to chemical and biochemical phenomena
-
Kollman, P. Free energy calculations: Applications to chemical and biochemical phenomena. Chem. Rev. 1993, 93, 2395-2417.
-
(1993)
Chem. Rev.
, vol.93
, pp. 2395-2417
-
-
Kollman, P.1
-
52
-
-
13444292556
-
Scoring functions for protein-ligand interactions: A critical perspective
-
Schulz-Gasch, T.; Stahl, M. Scoring Functions for Protein-Ligand Interactions: A Critical Perspective. DTT: Technol. 2004, 1, 231-239.
-
(2004)
DTT: Technol.
, vol.1
, pp. 231-239
-
-
Schulz-Gasch, T.1
Stahl, M.2
-
53
-
-
13344279324
-
Lead identification in post-genomics: Computers as a complementary alternative
-
Klebe, G. Lead Identification in Post-Genomics: Computers as a Complementary Alternative. DTT: Technol. 2004, 1, 225-230.
-
(2004)
DTT: Technol.
, vol.1
, pp. 225-230
-
-
Klebe, G.1
-
54
-
-
29144455862
-
-
Cohen, N. C., Ed.; Academic Press: San Diego, CA
-
Koehler, K. F.; Rao, S. N.; Snyder, J. P. In Guidebook on Molecular Modeling in Drug Design; Cohen, N. C., Ed.; Academic Press: San Diego, CA, 1996; pp 253-255.
-
(1996)
Guidebook on Molecular Modeling in Drug Design
, pp. 253-255
-
-
Koehler, K.F.1
Rao, S.N.2
Snyder, J.P.3
-
55
-
-
0031442549
-
A strategy for the incorporation of water molecules present in a ligand binding site into a three-dimensional quantitative structure-activity relationship analysis
-
Pastor, M.; Cruciani, G.; Watson, K. A Strategy for the Incorporation of Water Molecules Present in a Ligand Binding Site into a Three-Dimensional Quantitative Structure-Activity Relationship Analysis. J. Med. Chem. 1997, 40, 4089-4102.
-
(1997)
J. Med. Chem.
, vol.40
, pp. 4089-4102
-
-
Pastor, M.1
Cruciani, G.2
Watson, K.3
-
57
-
-
0029450365
-
Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions
-
Poornima, C. S.; Dean, P. M. Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions. J. Comput.-Aided Mol. Des. 1995, 9, 500-512.
-
(1995)
J. Comput.-Aided Mol. Des.
, vol.9
, pp. 500-512
-
-
Poornima, C.S.1
Dean, P.M.2
-
58
-
-
0029444719
-
Hydration in drug design. 2. Influence of local site surface shape on water binding
-
Poornima, C. S.; Dean, P. M. Hydration in drug design. 2. Influence of local site surface shape on water binding. J. Comput.-Aided Mol. Des. 1995, 9, 513-520.
-
(1995)
J. Comput.-Aided Mol. Des.
, vol.9
, pp. 513-520
-
-
Poornima, C.S.1
Dean, P.M.2
-
59
-
-
0029450636
-
Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins
-
Poornima, C. S.; Dean, P. M. Hydration in drug design. 3. Conserved water molecules at the ligand- binding sites of homologous proteins. J. Comput.-Aided Mol. Des. 1995, 9, 521-531.
-
(1995)
J. Comput.-Aided Mol. Des.
, vol.9
, pp. 521-531
-
-
Poornima, C.S.1
Dean, P.M.2
-
60
-
-
0034611597
-
Novel benzofuran and benzothiophene biphenyls as inhibitors of protein tyrosine phosphatase 1B with antihyperglycemic properties
-
Malamas, M. S.; Sredy, J.; Moxham, C.; Katz, A.; Xu, W.; McDevitt, R.; Adebayo, F. O.; Sawicki, D. R.; Seestaller, L.; Sullivan, D.; Taylor, J. R. Novel Benzofuran and Benzothiophene Biphenyls as Inhibitors of Protein Tyrosine Phosphatase 1B with Antihyperglycemic Properties. J. Med. Chem. 2000, 43, 1293-1310.
-
(2000)
J. Med. Chem.
, vol.43
, pp. 1293-1310
-
-
Malamas, M.S.1
Sredy, J.2
Moxham, C.3
Katz, A.4
Xu, W.5
McDevitt, R.6
Adebayo, F.O.7
Sawicki, D.R.8
Seestaller, L.9
Sullivan, D.10
Taylor, J.R.11
-
61
-
-
0034624722
-
New azolidinediones as inhibitors of protein tyrosine phosphatase 1B with antihyperglycemic properties
-
Malamas, M. S.; Sredy, J.; Gunawan, I.; Mihan, B.; Sawicki, D. R.; Seestaller, L.; Sullivan, D.; Flam, B. R. New Azolidinediones as Inhibitors of Protein Tyrosine Phosphatase 1B with Antihyperglycemic Properties. J. Med. Chem. 2000, 43, 995-1010.
-
(2000)
J. Med. Chem.
, vol.43
, pp. 995-1010
-
-
Malamas, M.S.1
Sredy, J.2
Gunawan, I.3
Mihan, B.4
Sawicki, D.R.5
Seestaller, L.6
Sullivan, D.7
Flam, B.R.8
-
62
-
-
0036715628
-
Protein tyrosine phosphatase 1b inhibitors for diabetes
-
Johnson, T. O.; Ermolieff, J.; Jirousek, M. R. Protein Tyrosine Phosphatase 1b Inhibitors for Diabetes. Nat. Rev. Drug Discovery 2002, 1, 696-709.
-
(2002)
Nat. Rev. Drug Discovery
, vol.1
, pp. 696-709
-
-
Johnson, T.O.1
Ermolieff, J.2
Jirousek, M.R.3
-
63
-
-
29144530135
-
-
Accelrys Inc.: San Diego, CA
-
CERIUS2 LigandFit User Manual; Accelrys Inc.: San Diego, CA, 2000; pp 3-48.
-
(2000)
CERIUS2 LigandFit User Manual
, pp. 3-48
-
-
-
64
-
-
11144255694
-
Evaluation of library ranking efficacy in virtual screening
-
Kontoyianni, M.; Sokol, G. S.; McClellan, L. M. Evaluation of Library Ranking Efficacy in Virtual Screening. J. Comput. Chem. 2004, 26, 11-22.
-
(2004)
J. Comput. Chem.
, vol.26
, pp. 11-22
-
-
Kontoyianni, M.1
Sokol, G.S.2
McClellan, L.M.3
-
65
-
-
15244346501
-
LigScore: A novel scoring function for predicting binding affinities
-
Krammer, A.; Kirchhoff, P. D.; Jiang, X.; Venkatachalam, C. M.; Waldman, M. LigScore: a novel scoring function for predicting binding affinities. J. Mol. Graphics Modell. 2005, 23, 395-407.
-
(2005)
J. Mol. Graphics Modell.
, vol.23
, pp. 395-407
-
-
Krammer, A.1
Kirchhoff, P.D.2
Jiang, X.3
Venkatachalam, C.M.4
Waldman, M.5
-
66
-
-
0036241840
-
3D-QSAR CoMFA and CoMSIA on protein tyrosine phosphatase 1B inhibitors
-
Murthy, V. S.; Kulkarni, V. M. 3D-QSAR CoMFA and CoMSIA on Protein Tyrosine Phosphatase 1B Inhibitors. Bioorg. Med. Chem. 2002, 10, 2267-2282.
-
(2002)
Bioorg. Med. Chem.
, vol.10
, pp. 2267-2282
-
-
Murthy, V.S.1
Kulkarni, V.M.2
-
67
-
-
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
-
68
-
-
0035811458
-
A new concept for multidimensional selection of ligand conformations (MultiSelect) and multidimensional scoring (MultiScore) of protein-ligand binding affinities
-
Terp, G. E.; Johansen, B. N.; Christensen, I. T.; Jorgensen, F. S. A new concept for multidimensional selection of ligand conformations (MultiSelect) and multidimensional scoring (MultiScore) of protein-ligand binding affinities. J. Med. Chem. 2001, 44, 2333-2343.
-
(2001)
J. Med. Chem.
, vol.44
, pp. 2333-2343
-
-
Terp, G.E.1
Johansen, B.N.2
Christensen, I.T.3
Jorgensen, F.S.4
-
69
-
-
0036606204
-
ConsDock: A new program for the consensus analysis of protein-ligand interactions
-
Paul, N.; Rognan, D. ConsDock: A new program for the consensus analysis of protein-ligand interactions. Proteins: Struct., Funct., Genet. 2002, 47, 521-533.
-
(2002)
Proteins: Struct., Funct., Genet.
, vol.47
, pp. 521-533
-
-
Paul, N.1
Rognan, D.2
-
70
-
-
3042832379
-
GPCRs: An update on structural approaches to drug discovery
-
Beeley, N. R. A.; Sage, C. GPCRs: an update on structural approaches to drug discovery. Targets 2003, 2, 19-25.
-
(2003)
Targets
, vol.2
, pp. 19-25
-
-
Beeley, N.R.A.1
Sage, C.2
-
71
-
-
29144505998
-
-
Harvey, A. L., Ed.; John Wiley & Sons: Chchester, U.K.
-
Waszkowycz, B. In Advances in Drug Discovery Techniques; Harvey, A. L., Ed.; John Wiley & Sons: Chchester, U.K., 1998; pp 150-153.
-
(1998)
Advances in Drug Discovery Techniques
, pp. 150-153
-
-
Waszkowycz, B.1
-
72
-
-
29144508664
-
-
Gundertofte, K., Jørgensen F. S., Eds.; Kluwer Academic/Olenum Publishers: New York
-
th European Symposium on Quantitative Structure-Activity Relationships: Molecular modeling and Prediction of Bioactivity; Gundertofte, K., Jørgensen F. S., Eds.; Kluwer Academic/Olenum Publishers: New York, 1998; pp 453-454.
-
(1998)
th European Symposium on Quantitative Structure-Activity Relationships: Molecular Modeling and Prediction of Bioactivity
, pp. 453-454
-
-
Drew, M.G.B.1
Lumley, N.R.2
Price, N.R.3
Watkins, R.W.4
-
73
-
-
0038724207
-
The importance of being earnest: Validation is the absolute essential for successful application and interpretation of QSPR models
-
Tropsha, A.; Gramatica, P.; Gombar, V. K. The Importance of Being Earnest: Validation is the Absolute Essential for Successful Application and Interpretation of QSPR Models. Quant. Struct.-Act. Relat. Comb. Sci. 2003, 22, 69-77.
-
(2003)
Quant. Struct.-Act. Relat. Comb. Sci.
, vol.22
, pp. 69-77
-
-
Tropsha, A.1
Gramatica, P.2
Gombar, V.K.3
-
74
-
-
0000125764
-
A new model for calculating atomic charges in molecules
-
Gasteiger J.; Marsili, M. A new model for calculating atomic charges in molecules. Tetrahedron Lett. 1978, 34, 3181-3184.
-
(1978)
Tetrahedron Lett.
, vol.34
, pp. 3181-3184
-
-
Gasteiger, J.1
Marsili, M.2
-
75
-
-
84890244523
-
-
Accelrys Inc.: San Diego, CA
-
CERIUS2 OFF; Accelrys Inc.: San Diego, CA, 1997; pp 5-109.
-
(1997)
CERIUS2 OFF
, pp. 5-109
-
-
-
76
-
-
29144525972
-
-
Accelrys Inc.: San Diego, CA
-
CERIUS2 4.8.1 QSAR; Accelrys Inc.: San Diego, CA, 2003; pp 161-171.
-
(2003)
CERIUS2 4.8.1 QSAR
, pp. 161-171
-
-
-
77
-
-
29144525972
-
-
Accelrys Inc.: San Diego, CA
-
CERIUS2 4.8.1 QSAR; Accelrys Inc.: San Diego, CA, 2003; pp 210-235.
-
(2003)
CERIUS2 4.8.1 QSAR
, pp. 210-235
-
-
-
78
-
-
0033949276
-
Receptor-based 3D QSAR analysis of estrogen receptor ligands-merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods
-
Sippl, W. Receptor-based 3D QSAR analysis of estrogen receptor ligands-merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods. J. Comput.-Aided Mol. Des. 2000, 14, 559-572.
-
(2000)
J. Comput.-Aided Mol. Des.
, vol.14
, pp. 559-572
-
-
Sippl, W.1
-
79
-
-
0027209171
-
The probability of chance correlation using partial least squares (PLS)
-
Clark, M.; Cramer, R. D. The probability of chance correlation using partial least squares (PLS). Quant. Struct.-Act. Relat. 1993, 12, 137-145.
-
(1993)
Quant. Struct.-Act. Relat.
, vol.12
, pp. 137-145
-
-
Clark, M.1
Cramer, R.D.2
|