-
1
-
-
34548324706
-
The cost of biopharmaceutical R&D: Is biotech different?
-
DiMasi, J.A.; Grabowski, H.G. The cost of biopharmaceutical R&D: Is biotech different? Managerial Dec. Econ., 2007, 28, 469-479.
-
(2007)
Managerial Dec. Econ
, vol.28
, pp. 469-479
-
-
DiMasi, J.A.1
Grabowski, H.G.2
-
2
-
-
65749102941
-
-
PhRMA Industry Profile 2008 Report, http://www.phrma.org/publications
-
PhRMA Industry Profile 2008 Report, http://www.phrma.org/publications
-
-
-
-
3
-
-
65749097979
-
-
Center for Drug Evaluation and Research: Http://www.fda.gov/cder/rdmt
-
-
-
-
4
-
-
32444441360
-
Computational chemistry-driven decision making in lead generation
-
Schnecke, V.; Boström, J. Computational chemistry-driven decision making in lead generation. Drug Discov. Today, 2006, 11, 43-50.
-
(2006)
Drug Discov. Today
, vol.11
, pp. 43-50
-
-
Schnecke, V.1
Boström, J.2
-
5
-
-
0034581968
-
High-throughput and virtual. screening: Core lead discovery technologies move towards integration
-
Good, A.C.; Krystek, S.R.; Mason, J.S. High-throughput and virtual. screening: Core lead discovery technologies move towards integration. Drug Discov. Today, 2000, 5, S61-S69.
-
(2000)
Drug Discov. Today
, vol.5
-
-
Good, A.C.1
Krystek, S.R.2
Mason, J.S.3
-
6
-
-
33645204379
-
The design and docking of virtual compound libraries to structure of drug targets
-
Anderson, A.C.; Wright, D.L. The design and docking of virtual compound libraries to structure of drug targets. Curr. Comput. Aided Drug Des., 2005, 1, 103-127.
-
(2005)
Curr. Comput. Aided Drug Des
, vol.1
, pp. 103-127
-
-
Anderson, A.C.1
Wright, D.L.2
-
7
-
-
0031024171
-
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
-
Lipinski, C.A.; Lombardo, F.; Dominy, B.W.; Feeney, P.J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev., 1997, 23, 3-25.
-
(1997)
Adv. Drug Deliv. Rev
, vol.23
, pp. 3-25
-
-
Lipinski, C.A.1
Lombardo, F.2
Dominy, B.W.3
Feeney, P.J.4
-
8
-
-
42749090651
-
Is it possible to increase hit rates in structure-based virtual screening by pharmacophore filtering? An investigation of the advantages and pitfalls of post-filtering
-
Muthas, D.; Sabnis, Y.A.; Lundborg, M.; Karlén, A. Is it possible to increase hit rates in structure-based virtual screening by pharmacophore filtering? An investigation of the advantages and pitfalls of post-filtering. J. Mol. Graphics Model., 2008, 26, 1237-1251.
-
(2008)
J. Mol. Graphics Model
, vol.26
, pp. 1237-1251
-
-
Muthas, D.1
Sabnis, Y.A.2
Lundborg, M.3
Karlén, A.4
-
9
-
-
8844263008
-
Docking and scoring in virtual screening for drug discovery: Methods and applications
-
Kitchen, D.B.; Decornez, H.; Furr, J.R.; Bajorath, J. Docking and scoring in virtual screening for drug discovery: Methods and applications. Nature Rev. Drug Discov., 2004, 3, 935-949.
-
(2004)
Nature Rev. Drug Discov
, vol.3
, pp. 935-949
-
-
Kitchen, D.B.1
Decornez, H.2
Furr, J.R.3
Bajorath, J.4
-
11
-
-
41349090342
-
Can we use docking and scoring for hit-to-lead optimization?
-
Enyedy, I.J.; Egan, W.J. Can we use docking and scoring for hit-to-lead optimization? J. Comput. Aided. Mol. Des., 2008, 28, 161-168.
-
(2008)
J. Comput. Aided. Mol. Des
, vol.28
, pp. 161-168
-
-
Enyedy, I.J.1
Egan, W.J.2
-
12
-
-
33749245117
-
Prediction of protein-ligand interactions. Docking and scoring: Successes and gaps
-
Leach, A.R.; Shoichet, B.K.; Peishoff, C.E. Prediction of protein-ligand interactions. Docking and scoring: Successes and gaps. J. Med. Chem.,, 2006, 49, 5851-5855.
-
(2006)
J. Med. Chem
, vol.49
, pp. 5851-5855
-
-
Leach, A.R.1
Shoichet, B.K.2
Peishoff, C.E.3
-
13
-
-
14044262243
-
Successes and challenges
-
Mohan, V.; Gibbs, A.C.; Cummings, M.D.; Jaeger, E.P.; DesJarlais, R.L. Docking: Successes and challenges. Curr. Pharm. Des., 2005, 11, 323-333.
-
(2005)
Curr. Pharm. Des
, vol.11
, pp. 323-333
-
-
Mohan, V.1
Gibbs, A.C.2
Cummings, M.D.3
Jaeger, E.P.4
DesJarlais5
Docking, R.L.6
-
14
-
-
40349087133
-
Towards the development of universal, fast and highly accurate docking/ scoring methods: A long way to go
-
Moitessier, N.; Englebienne, P.; Lee, D.; Lawandi, J.; and Corbeil, C.R. Towards the development of universal, fast and highly accurate docking/ scoring methods: A long way to go. Br. J. Pharmacol., 2008, 153, S7-S26.
-
(2008)
Br. J. Pharmacol
, vol.153
-
-
Moitessier, N.1
Englebienne, P.2
Lee, D.3
Lawandi, J.4
Corbeil, C.R.5
-
15
-
-
34249846647
-
Artificial Intelligence Approaches for Rational Drug Design and Discovery
-
Duch, W.; Swaminathan, K.; Meller, J. Artificial Intelligence Approaches for Rational Drug Design and Discovery. Curr. Pharm. Des., 2007, 13, 1497-1508.
-
(2007)
Curr. Pharm. Des
, vol.13
, pp. 1497-1508
-
-
Duch, W.1
Swaminathan, K.2
Meller, J.3
-
18
-
-
0003922190
-
-
2nd ed, Wiley, J, New York
-
Duda R.O.; Hart P.E.; Stork D.G. Pattern classification, 2nd ed., Wiley, J., New York, 2001.
-
(2001)
Pattern classification
-
-
Duda, R.O.1
Hart, P.E.2
Stork, D.G.3
-
21
-
-
0036606483
-
Principles of Docking: An Overviewof Search Algorithms and a Guide to Scoring Functions
-
Halperin, I.; Ma, B.; Wolfson, H.; Nussinov, R. Principles of Docking: An Overviewof Search Algorithms and a Guide to Scoring Functions. Proteins: Struc. Func. Genet., 2002, 47, 409-443.
-
(2002)
Proteins: Struc. Func. Genet
, vol.47
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
22
-
-
33947536095
-
In Silico screening of ligand databases: Methods and applications
-
Khedkar, S.A.; Malde, A.K.; Coutinho, E.C. In Silico screening of ligand databases: Methods and applications. Ind. J. Pharmaceut. Sci., 2008, 68, 689-696.
-
(2008)
Ind. J. Pharmaceut. Sci
, vol.68
, pp. 689-696
-
-
Khedkar, S.A.1
Malde, A.K.2
Coutinho, E.C.3
-
23
-
-
29044433371
-
Recent advances in docking and scoring
-
Krovat, E.M.; Steindl, T.; Langer, T. Recent advances in docking and scoring. Curr. Comp. Aided Drug Des., 2005, 1, 93-102.
-
(2005)
Curr. Comp. Aided Drug Des
, vol.1
, pp. 93-102
-
-
Krovat, E.M.1
Steindl, T.2
Langer, T.3
-
24
-
-
84892166712
-
Einfluss der configuration auf die wirkung der enzyme.
-
Fischer, E. Einfluss der configuration auf die wirkung der enzyme. Ber. 1894, 27, 2985-2993.
-
(1894)
Ber
, vol.27
, pp. 2985-2993
-
-
Fischer, E.1
-
25
-
-
0001858251
-
Application of a theory of enzyme specificity to protein synthesis
-
Koshland, D.E. Jr. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. USA, 1958, 44, 98-104.
-
(1958)
Proc. Natl. Acad. Sci. USA
, vol.44
, pp. 98-104
-
-
Koshland Jr., D.E.1
-
26
-
-
0027943261
-
Conformational isomerism and the diversity of antibodies
-
Foote J; Milstein C. Conformational isomerism and the diversity of antibodies. Proc. Natl. Acad. Sci. USA, 1994, 91, 10370-7435.
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 10370-17435
-
-
Foote, J.1
Milstein, C.2
-
27
-
-
33749449880
-
Docking and Scoring - Theoretically Easy, Practically Impossible?
-
Coupez, B.; Lewis, R.A. Docking and Scoring - Theoretically Easy, Practically Impossible? Curr. Med. Chem., 2006, 13, 2995-3003.
-
(2006)
Curr. Med. Chem
, vol.13
, pp. 2995-3003
-
-
Coupez, B.1
Lewis, R.A.2
-
28
-
-
0038460858
-
Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes
-
McGovern, S.L.; Shoichet, B.K. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J. Med. Chem., 2003, 46, 2895-2907.
-
(2003)
J. Med. Chem
, vol.46
, pp. 2895-2907
-
-
McGovern, S.L.1
Shoichet, B.K.2
-
29
-
-
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
-
30
-
-
0037235663
-
Protein-based virtual screening of chemical databases. II. Are homology models of G-protein coupled receptors suitable targets?
-
Bissantz, C.; Bernard, P.; Hibert, M.; Rognan, D. Protein-based virtual screening of chemical databases. II. Are homology models of G-protein coupled receptors suitable targets? Proteins, 2003, 50, 5-25.
-
(2003)
Proteins
, vol.50
, pp. 5-25
-
-
Bissantz, C.1
Bernard, P.2
Hibert, M.3
Rognan, D.4
-
31
-
-
33645218742
-
High-throughput screening of biocatalytic activity: Applications in drug discovery
-
Kumar, R.A.; Clark, D.S. High-throughput screening of biocatalytic activity: Applications in drug discovery. Curr. Opin. Chem. Biol., 2006, 10, 162-168.
-
(2006)
Curr. Opin. Chem. Biol
, vol.10
, pp. 162-168
-
-
Kumar, R.A.1
Clark, D.S.2
-
32
-
-
0001971367
-
The nature of the intermolecular forces operative in biological processes
-
Pauling L.; Delbrück M. The nature of the intermolecular forces operative in biological processes. Science, 1940, 92, 77-79.
-
(1940)
Science
, vol.92
, pp. 77-79
-
-
Pauling, L.1
Delbrück, M.2
-
33
-
-
0008863560
-
Some factors in the interpretation of protein denaturation
-
Kauzmann W. Some factors in the interpretation of protein denaturation. Adv. Protein Chem., 1959, 14, 1-63.
-
(1959)
Adv. Protein Chem
, vol.14
, pp. 1-63
-
-
Kauzmann, W.1
-
35
-
-
65749092614
-
-
Hecht, D.; Rios-Reyes, E. Data presented at 29th West Coast Biological Sciences Undergraduate Research Symposium at Point Loma Nazarene University in 2006.
-
Hecht, D.; Rios-Reyes, E. Data presented at 29th West Coast Biological Sciences Undergraduate Research Symposium at Point Loma Nazarene University in 2006.
-
-
-
-
36
-
-
0026813925
-
The Computer Program Ludi: A New Method for the de Novo Design of Enzyme Inhibitors
-
Böhm 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
-
-
Böhm, H.J.1
-
37
-
-
0028454828
-
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional sturcture
-
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 sturcture. J. Comput. Aided Mol. Des., 1994, 8, 243.
-
(1994)
J. Comput. Aided Mol. Des
, vol.8
, pp. 243
-
-
Böhm, H.J.1
-
38
-
-
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.; Olsen, A.J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem., 1998, 9, 1639-1662.
-
(1998)
J. Comput. Chem
, vol.9
, 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
Olsen, A.J.7
-
39
-
-
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
-
41
-
-
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
-
42
-
-
12144289984
-
A new approach for rapid, accurate docking and scoring. 1. method and assessment of 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 of 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
Shenkin13
Glide, P.S.14
-
43
-
-
33750124980
-
Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes
-
Friesner, R.A.; Murphy, R.B.; Repasky, M.P.; Frye, L.L.; Greenwood, J.R.; Halgren, T.A.; Sanschagrin, P.C.; Mainz, D.T. Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J. Med. Chem., 2006, 49, 6177-6196.
-
(2006)
J. Med. Chem
, vol.49
, pp. 6177-6196
-
-
Friesner, R.A.1
Murphy, R.B.2
Repasky, M.P.3
Frye, L.L.4
Greenwood, J.R.5
Halgren, T.A.6
Sanschagrin, P.C.7
Mainz, D.T.8
-
44
-
-
0030255303
-
Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities
-
Jain, A.N. Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities. J. Comput. Aided. Mol. Des., 1996, 10, 427-440.
-
(1996)
J. Comput. Aided. Mol. Des
, vol.10
, pp. 427-440
-
-
Jain, A.N.1
-
45
-
-
0037030649
-
Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 1. models without explicit constrained water
-
Cozzini P.; Fornabaio M.; Marabotti A.; Abraham D.J.; Kellogg G.E.; Mozzarelli A. Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 1. models without explicit constrained water. J. Med. Chem., 2002, 45, 2469-2483.
-
(2002)
J. Med. Chem
, vol.45
, pp. 2469-2483
-
-
Cozzini, P.1
Fornabaio, M.2
Marabotti, A.3
Abraham, D.J.4
Kellogg, G.E.5
Mozzarelli, A.6
-
46
-
-
15244346501
-
-
Krammer, A.; Kirchhoff, P.D.; Jiang, X.; Venkatachalam, C.M.; Waldman, M. LigScore: A novel scoring function for predicting binding affinities. J. Mol. Graph. Model., 2005, 23, 395-407.
-
Krammer, A.; Kirchhoff, P.D.; Jiang, X.; Venkatachalam, C.M.; Waldman, M. LigScore: A novel scoring function for predicting binding affinities. J. Mol. Graph. Model., 2005, 23, 395-407.
-
-
-
-
47
-
-
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, 317-24.
-
(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
-
48
-
-
0001704085
-
SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex
-
Wang R.; Liu L.; Lai L.; Tang Y. SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex. J. Mol. Mod., 1998, 4, 379-394.
-
(1998)
J. Mol. Mod
, vol.4
, pp. 379-394
-
-
Wang, R.1
Liu, L.2
Lai, L.3
Tang, Y.4
-
49
-
-
33644843080
-
PSI-DOCK: Towards highly efficient and accurate flexible ligand docking
-
Pei J.; Wang Q.; Liu Z.; Li Q.; Yang K.; Lai L. PSI-DOCK: Towards highly efficient and accurate flexible ligand docking. Proteins Struct. Funct. Genet., 2006, 62, 934-946.
-
(2006)
Proteins Struct. Funct. Genet
, vol.62
, pp. 934-946
-
-
Pei, J.1
Wang, Q.2
Liu, Z.3
Li, Q.4
Yang, K.5
Lai, L.6
-
50
-
-
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
-
51
-
-
33846863158
-
Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. exploring the parameter space
-
Naim, M.; Bhat, S.; Rankin, K.N.; Dennis, S.; Chowdhury, S.F.; Siddiqi, I.; Drabik, P.; Sulea, T.; Bayly, C.I.; Jakalian, A.; Purisima, E.O. Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. exploring the parameter space. J. Chem. Inf. Model., 2007, 47, 122-133.
-
(2007)
J. Chem. Inf. Model
, vol.47
, pp. 122-133
-
-
Naim, M.1
Bhat, S.2
Rankin, K.N.3
Dennis, S.4
Chowdhury, S.F.5
Siddiqi, I.6
Drabik, P.7
Sulea, T.8
Bayly, C.I.9
Jakalian, A.10
Purisima, E.O.11
-
52
-
-
0036022960
-
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
-
Wang R.; Lai L.;Wang S. Further development and validation of empirical scoring functions for structure-based binding 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
-
53
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks, B.R.; Bruccoleri, R.E.; Olafson, B.D.; States, D.J.; Swaminathan, S.; Karplus, M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem., 1983, 4, 187-217.
-
(1983)
J. Comp. Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
54
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell, W.D.; Cieplak, P.; Bayly, C.I.; Gould, I.R.; Merz, K.M.; Ferguson, D.M.; Spellmeyer, D.C.; Fox, T.; Caldwell, J.W.; Kollman, P.A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc., 1995, 117, 5179.
-
(1995)
J. Am. Chem. Soc
, vol.117
, pp. 5179
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
55
-
-
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
-
56
-
-
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
-
57
-
-
0028854034
-
Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
-
Jones, G.; Willett, P.; Glen, R.C. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J. Mol. Biol., 1995, 245, 43-53.
-
(1995)
J. Mol. Biol
, vol.245
, pp. 43-53
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
-
58
-
-
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
-
59
-
-
84986522918
-
ICM - a new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
-
Abagyan R.; Totrov M.; Kuznetsov D. ICM - a new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation. J. Comput. Chem., 1994, 15, 488-506.
-
(1994)
J. Comput. Chem
, vol.15
, pp. 488-506
-
-
Abagyan, R.1
Totrov, M.2
Kuznetsov, D.3
-
60
-
-
0031181346
-
Powerful, rapid computer algorithms for structure-based drug design
-
McMartin C.; Bohacek R.S. QXP: Powerful, rapid computer algorithms for structure-based drug design. J. Comput. Aided. Mol. Des., 1997, 11, 333-344.
-
(1997)
J. Comput. Aided. Mol. Des
, vol.11
, pp. 333-344
-
-
McMartin, C.1
Bohacek, R.S.Q.2
-
61
-
-
33749266178
-
A method for induced-fit docking, scoring, and ranking of flexible ligands. Application to peptide and pseudopeptidic β-secretase (BACE 1) inhibitors
-
Moitessier N.; Therrien E.; Hanessian S. A method for induced-fit docking, scoring, and ranking of flexible ligands. Application to peptide and pseudopeptidic β-secretase (BACE 1) inhibitors. J. Med. Chem., 2006, 49, 5885-5894.
-
(2006)
J. Med. Chem
, vol.49
, pp. 5885-5894
-
-
Moitessier, N.1
Therrien, E.2
Hanessian, S.3
-
62
-
-
0029995624
-
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.; Marshall, G.R. A new method for the receptor-based prediction of binding affinities of novel ligands. J. Am. Chem. Soc., 1996, 118, 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
-
63
-
-
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, i 295, 337-356.
-
(2000)
J. Mol. Biol
, vol.1
, Issue.295
, pp. 337-356
-
-
Gohlke, H.1
Hendlich, M.2
Klebe, G.3
-
64
-
-
26444588137
-
DrugScore(CSD)-Knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction
-
Velec, H.F.G.; Gohlke, H.; Klebe, G. DrugScore(CSD)-Knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. J. Med. Chem., 2005, 48, 6296-6303.
-
(2005)
J. Med. Chem
, vol.48
, pp. 6296-6303
-
-
Velec, H.F.G.1
Gohlke, H.2
Klebe, G.3
-
65
-
-
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. 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.5
-
66
-
-
33749239216
-
A new knowledge-based potential scoring function accounting for protein atom mobility
-
Yang C.Y.; Wang, R.; Wang, S. M-Score: A new knowledge-based potential scoring function accounting for protein atom mobility. J. Med. Chem., 2006, 49, 5903-5911.
-
(2006)
J. Med. Chem
, vol.49
, pp. 5903-5911
-
-
Yang, C.Y.1
Wang, R.2
Wang3
M-Score, S.4
-
67
-
-
0031717170
-
Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization
-
Schaffer, L.; Verkhivker, G.M. Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization. Proteins, 1998, 33, 295-310.
-
(1998)
Proteins
, vol.33
, pp. 295-310
-
-
Schaffer, L.1
Verkhivker, G.M.2
-
68
-
-
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
-
69
-
-
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 Discov. Des., 2000, 20, 99-114.
-
(2000)
Perspect. Drug Discov. Des
, vol.20
, pp. 99-114
-
-
Muegge, I.1
-
70
-
-
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
-
71
-
-
33846487854
-
-
Muegge, I.; Oloff, S. Advances in virtual screening. Drug Discov. Today Technol., 2006, 3, 405-411.
-
Muegge, I.; Oloff, S. Advances in virtual screening. Drug Discov. Today Technol., 2006, 3, 405-411.
-
-
-
-
72
-
-
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
-
73
-
-
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
-
74
-
-
0037161605
-
Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-IB
-
Doman, T. N.; McGovern, S.L.; Witherbee, B.J.; Kasten, T.P.; Kurumbail, R.; Stallings, W.C.; Connolly, D.T.; Shoichet, B.K. Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-IB. J. Med. Chem., 2002, 45, 2213-2221.
-
(2002)
J. Med. Chem
, vol.45
, pp. 2213-2221
-
-
Doman, T.N.1
McGovern, S.L.2
Witherbee, B.J.3
Kasten, T.P.4
Kurumbail, R.5
Stallings, W.C.6
Connolly, D.T.7
Shoichet, B.K.8
-
75
-
-
0031135364
-
A comparison of heuristic search algorithms for molecular docking
-
Westhead, D.R.; Clark, D.E.; Murray, C.W. A comparison of heuristic search algorithms for molecular docking. J. Comput. Aided. Mol. Des., 1997, 11, 209-228.
-
(1997)
J. Comput. Aided. Mol. Des
, vol.11
, pp. 209-228
-
-
Westhead, D.R.1
Clark, D.E.2
Murray, C.W.3
-
76
-
-
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
-
77
-
-
0035829446
-
Evaluation of scoring functions for protein-ligand docking
-
Perez, C.; Ortiz, A.R. Evaluation of scoring functions for protein-ligand docking. J. Med. Chem., 2001, 44, 3768-3785.
-
(2001)
J. Med. Chem
, vol.44
, pp. 3768-3785
-
-
Perez, C.1
Ortiz, A.R.2
-
78
-
-
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.; Jørgensen, 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
Jørgensen, F.S.4
-
79
-
-
0142028937
-
Kinases, homology models, and high throughput docking
-
Diller, D.J.; Li, R. Kinases, homology models, and high throughput docking. J. Med. Chem., 2003, 46, 4638-4647.
-
(2003)
J. Med. Chem
, vol.46
, pp. 4638-4647
-
-
Diller, D.J.1
Li, R.2
-
80
-
-
0037235881
-
Virtual screening to enrich hit lists from high-throughput screening: A case study on small-molecule inhibitors of angiogenin
-
Jenkins, J.L.; Kao, R.Y.T; Shapiro, R. Virtual screening to enrich hit lists from high-throughput screening: A case study on small-molecule inhibitors of angiogenin. Proteins Struct. Funct. Genet., 2003, 50, 81-93.
-
(2003)
Proteins Struct. Funct. Genet
, vol.50
, pp. 81-93
-
-
Jenkins, J.L.1
Kao, R.Y.T.2
Shapiro, R.3
-
81
-
-
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. Mod., 2003, 9, 47-57.
-
(2003)
J. Mol. Mod
, vol.9
, pp. 47-57
-
-
Schulz-Gasch, T.1
Stahl, M.2
-
82
-
-
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
-
83
-
-
10044294023
-
An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes
-
Wang, R.; Lu, Y.; Fang, X.; Wang, S. An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes. J. Chem. Inf. Comput. Sci., 2004, 44, 2114-2125.
-
(2004)
J. Chem. Inf. Comput. Sci
, vol.44
, pp. 2114-2125
-
-
Wang, R.1
Lu, Y.2
Fang, X.3
Wang, S.4
-
84
-
-
1942471391
-
Assessing scoring functions for protein- ligand interactions
-
Ferrara, P.; Gohlke, H.; Price, D.J.; Klebe, G.; Brooks, C.L. III. Assessing scoring functions for protein- ligand interactions. J. Med. Chem., 2004, 47, 3032-3047.
-
(2004)
J. Med. Chem
, vol.47
, pp. 3032-3047
-
-
Ferrara, P.1
Gohlke, H.2
Price, D.J.3
Klebe, G.4
Brooks III, C.L.5
-
85
-
-
4544367743
-
Comparative evaluation of eight docking tools for docking and virtual screening
-
Kellenberger, E.; Rodrigo, J.; Muller, P.; Rognan, D. Comparative evaluation of eight docking tools for docking and virtual screening. Proteins Struct. Funct. Genet., 2004, 57, 225-242.
-
(2004)
Proteins Struct. Funct. Genet
, vol.57
, pp. 225-242
-
-
Kellenberger, E.1
Rodrigo, J.2
Muller, P.3
Rognan, D.4
-
86
-
-
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
-
87
-
-
2942706223
-
Assessment of docking poses: Interactions-based accuracy classification (IBAC) vs crystal structure deviations
-
Kroemer, R.T.; Vulpetti, A.; McDonald, J.J.; Rohrer, D.C.; Trosset, J.Y.; Giordanetto, F.; Cotesta, S.; McMartin, C.; Kihlén, M.; Stouten, P.F. Assessment of docking poses: Interactions-based accuracy classification (IBAC) vs crystal structure deviations. J. Chem. Inf. Comput. Sci., 2004, 44, 871-881.
-
(2004)
J. Chem. Inf. Comput. Sci
, vol.44
, pp. 871-881
-
-
Kroemer, R.T.1
Vulpetti, A.2
McDonald, J.J.3
Rohrer, D.C.4
Trosset, J.Y.5
Giordanetto, F.6
Cotesta, S.7
McMartin, C.8
Kihlén, M.9
Stouten, P.F.10
-
88
-
-
3042806401
-
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
-
Perola, E.; Walters, W.P.; Charifson, P.S. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins Struct. Funct. Genet., 2004, 56, 235-249.
-
(2004)
Proteins Struct. Funct. Genet
, vol.56
, pp. 235-249
-
-
Perola, E.1
Walters, W.P.2
Charifson, P.S.3
-
89
-
-
33244483907
-
On evaluating molecular-docking methods for pose prediction and enrichment factors
-
Chen, H.; Lyne, P.D.; Giordanetto, F.; Lovell, T.; Li, J. On evaluating molecular-docking methods for pose prediction and enrichment factors J. Chem. Inf. Model., 2006, 46 401-415.
-
(2006)
J. Chem. Inf. Model
, vol.46
, pp. 401-415
-
-
Chen, H.1
Lyne, P.D.2
Giordanetto, F.3
Lovell, T.4
Li, J.5
-
90
-
-
13944263886
-
Comparison of automated docking programs as virtual screening tools
-
Cummings, M.D.; DesJarlais, R.L.; Gibbs, A.C.; Mohan, V.; Jaeger, E.P. Comparison of automated docking programs as virtual screening tools. J. Med. Chem., 2005, 48, 962-976.
-
(2005)
J. Med. Chem
, vol.48
, pp. 962-976
-
-
Cummings, M.D.1
DesJarlais, R.L.2
Gibbs, A.C.3
Mohan, V.4
Jaeger, E.P.5
-
91
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
Warren, G.L.; Andrews, C.W.; Capelli, A.M.; Clarke, B.; LaLonde, J.; Lambert, M.H.; Lindvall, M.; Nevins, N.; Semus, S.F.; Senger, S.; Tedesco, G.; Wall, I.D.; Woolven, J.M.; Peishoff, C.E.; Head, M.S. A critical assessment of docking programs and scoring functions. J. Med. Chem., 2006, 49, 5912-5931.
-
(2006)
J. Med. Chem
, vol.49
, pp. 5912-5931
-
-
Warren, G.L.1
Andrews, C.W.2
Capelli, A.M.3
Clarke, B.4
LaLonde, J.5
Lambert, M.H.6
Lindvall, M.7
Nevins, N.8
Semus, S.F.9
Senger, S.10
Tedesco, G.11
Wall, I.D.12
Woolven, J.M.13
Peishoff, C.E.14
Head, M.S.15
-
92
-
-
34547661861
-
Comparative performance of several flexible docking programs and scoring functions: Fnrichment dtudies for a diverse set of pharmaceutically relevant targets
-
Zhou, Z.; Felts, A.K.; Friesner, R.A.; Levy, R.M. Comparative performance of several flexible docking programs and scoring functions: fnrichment dtudies for a diverse set of pharmaceutically relevant targets. J. Chem. Inf. Model., 2007, 47, 1599-1608.
-
(2007)
J. Chem. Inf. Model
, vol.47
, pp. 1599-1608
-
-
Zhou, Z.1
Felts, A.K.2
Friesner, R.A.3
Levy, R.M.4
-
93
-
-
34247260419
-
Comments on the article On evaluating molecular-docking methods for pose prediction and enrichment factors
-
Perola E.; Walters W.P.; Charifson P. Comments on the article "On evaluating molecular-docking methods for pose prediction and enrichment factors." J. Chem. Inf. Model., 2007, 47, 251-253.
-
(2007)
J. Chem. Inf. Model
, vol.47
, pp. 251-253
-
-
Perola, E.1
Walters, W.P.2
Charifson, P.3
-
94
-
-
41349106585
-
Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection - What can we learn from earlier mistakes?
-
Kirchmair, J.; Markt, P.; Distinto, S.; Wolber, G.; Langer, T. Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection - What can we learn from earlier mistakes? J. Comput. Aided Mol. Des., 2008, 22, 213-228.
-
(2008)
J. Comput. Aided Mol. Des
, vol.22
, pp. 213-228
-
-
Kirchmair, J.1
Markt, P.2
Distinto, S.3
Wolber, G.4
Langer, T.5
-
95
-
-
41349110382
-
How to do an evaluation: Pitfalls and traps
-
Hawkins, P.C.D.; Warren, G.L.; Skillman, A.G.; Nicholls, A. How to do an evaluation: Pitfalls and traps. J. Comput. Aided Mol. Des., 2008, 22, 179-190.
-
(2008)
J. Comput. Aided Mol. Des
, vol.22
, pp. 179-190
-
-
Hawkins, P.C.D.1
Warren, G.L.2
Skillman, A.G.3
Nicholls, A.4
-
96
-
-
34547673017
-
Comparison of Topological, Shape, and Docking Methods in Virtual Screening
-
McGaughey G.B.; Sheridan R.P.; Bayly C.I.; Culberson J.C.; Kreatsoulas C.; Lindsley S.; Maiorov V.; Truchon J.F.; Cornell W.D. Comparison of Topological, Shape, and Docking Methods in Virtual Screening. J. Chem. Inf. Model., 2007, 47, 1504-1519.
-
(2007)
J. Chem. Inf. Model
, vol.47
, pp. 1504-1519
-
-
McGaughey, G.B.1
Sheridan, R.P.2
Bayly, C.I.3
Culberson, J.C.4
Kreatsoulas, C.5
Lindsley, S.6
Maiorov, V.7
Truchon, J.F.8
Cornell, W.D.9
-
97
-
-
34547670476
-
Evaluations of molecular docking programs for virtual screening
-
Onodera K.; Satou K.; Hirota H. Evaluations of molecular docking programs for virtual screening. J. Chem. Inf. Model. 2007, 47, 1609-1618.
-
(2007)
J. Chem. Inf. Model
, vol.47
, pp. 1609-1618
-
-
Onodera, K.1
Satou, K.2
Hirota, H.3
-
98
-
-
20144378530
-
Decoys for docking
-
Graves, A.P.; Brenk, R.; Shoichet, B.K. Decoys for docking J. Med. Chem., 2005, 48, 3714.
-
(2005)
J. Med. Chem
, vol.48
, pp. 3714
-
-
Graves, A.P.1
Brenk, R.2
Shoichet, B.K.3
-
99
-
-
34248562742
-
-
Grosdidier A.; Zoete V.; Michielin, O. EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization. Proteins Struct. Funct. Genet., 2007, 67, 1010-1025.
-
Grosdidier A.; Zoete V.; Michielin, O. EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization. Proteins Struct. Funct. Genet., 2007, 67, 1010-1025.
-
-
-
-
100
-
-
34548200847
-
Structure-based drug design: Docking and dcoring
-
Kroemer, R.T. Structure-based drug design: Docking and dcoring. Curr. Protein Pept. Sci., 2007, 8, 312-328.
-
(2007)
Curr. Protein Pept. Sci
, vol.8
, pp. 312-328
-
-
Kroemer, R.T.1
-
101
-
-
3342933156
-
Target-biased scoring approaches and expert systems in structure-based virtual screening
-
Jansen, J.M.; Martin, E.J. Target-biased scoring approaches and expert systems in structure-based virtual screening. Curr. Opin. Chem. Biol., 2004, 8, 359-364.
-
(2004)
Curr. Opin. Chem. Biol
, vol.8
, pp. 359-364
-
-
Jansen, J.M.1
Martin, E.J.2
-
102
-
-
38649091945
-
Modeling the inhibition of quadruple mutant Plasmodium falciparum dihydrofolate reductase by pyrimethamine derivatives
-
Fogel, G.B.; Cheung, M.;Pittman, E.; Hecht, D. Modeling the inhibition of quadruple mutant Plasmodium falciparum dihydrofolate reductase by pyrimethamine derivatives. J. Comput. Aided. Mol. Des., 2008, 22, 29-38.
-
(2008)
J. Comput. Aided. Mol. Des
, vol.22
, pp. 29-38
-
-
Fogel, G.B.1
Cheung, M.2
Pittman, E.3
Hecht, D.4
-
103
-
-
33744826819
-
MolDock: A new technique for high-accuracy molecular docking
-
Thomsen R.; Christensen M.H. MolDock: A new technique for high-accuracy molecular docking. J. Med. Chem., 2006, 49, 3315-3321.
-
(2006)
J. Med. Chem
, vol.49
, pp. 3315-3321
-
-
Thomsen, R.1
Christensen, M.H.2
-
104
-
-
0033576680
-
Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
-
Charifson, P.S.; Corkery, J.J.; Murcko, M.A.; Walters, W.P. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J. Med. Chem., 1999, 42, 5100-5109.
-
(1999)
J. Med. Chem
, vol.42
, pp. 5100-5109
-
-
Charifson, P.S.1
Corkery, J.J.2
Murcko, M.A.3
Walters, W.P.4
-
105
-
-
23844555629
-
Consensus scoring criteria for improving enrichment in virtual screening
-
Yang, J.M.; Chen, Y.F.; Shen, T.W.; Kristal, B.S.; Hsu, D.F. Consensus scoring criteria for improving enrichment in virtual screening. J. Chem. Inf. Model., 2005, 45, 1134.
-
(2005)
J. Chem. Inf. Model
, vol.45
, pp. 1134
-
-
Yang, J.M.1
Chen, Y.F.2
Shen, T.W.3
Kristal, B.S.4
Hsu, D.F.5
-
106
-
-
45949096079
-
Computational intelligence approaches for pattern discovery in biological systems
-
Fogel, G.B. Computational intelligence approaches for pattern discovery in biological systems. Brief Bioinform., 2008, 9, 307-316.
-
(2008)
Brief Bioinform
, vol.9
, pp. 307-316
-
-
Fogel, G.B.1
-
107
-
-
0035860537
-
Machine learning for science: State of the art and future prospects
-
Mjolsness E; DeCoste D. Machine learning for science: State of the art and future prospects. Science, 2001, 293, 2051-5.
-
(2001)
Science
, vol.293
, pp. 2051-2055
-
-
Mjolsness, E.1
DeCoste, D.2
-
108
-
-
0242677271
-
A quantitative approach to biochemical structure-activity relationships
-
Hansch, C. A quantitative approach to biochemical structure-activity relationships. Acc.Chem. Res., 1969, 2, 232-239.
-
(1969)
Acc.Chem. Res
, vol.2
, pp. 232-239
-
-
Hansch, C.1
-
110
-
-
0035272009
-
A quantum mechanical/neural net model for boiling points with error estimation
-
Chalk, A.J.; Beck, B.; Clark, T. A quantum mechanical/neural net model for boiling points with error estimation. J. Chem. Inf. Comput. Sci., 2001, 41, 457-462.
-
(2001)
J. Chem. Inf. Comput. Sci
, vol.41
, pp. 457-462
-
-
Chalk, A.J.1
Beck, B.2
Clark, T.3
-
111
-
-
18344410789
-
Toward generating simpler QSAR models: Non-linear multivariate regression vs several neural network ensembles and some related methods
-
Lučić, B.; Nadramija, D.; Bašic, I.; Tranajstić, N. Toward generating simpler QSAR models: Non-linear multivariate regression vs several neural network ensembles and some related methods. J. Chem. Inf. Comput. Sci., 2003, 43, 1094-1102.
-
(2003)
J. Chem. Inf. Comput. Sci
, vol.43
, pp. 1094-1102
-
-
Lučić, B.1
Nadramija, D.2
Bašic, I.3
Tranajstić, N.4
-
112
-
-
0037352051
-
Prediction of dihydrofolate reductase inhibition and selectivity using computational neural networks and linear discriminant analysis
-
Mattioni, B.E.; Jurs, P.C. Prediction of dihydrofolate reductase inhibition and selectivity using computational neural networks and linear discriminant analysis. J. Mol. Graphics Model., 2003, 21, 391-419.
-
(2003)
J. Mol. Graphics Model
, vol.21
, pp. 391-419
-
-
Mattioni, B.E.1
Jurs, P.C.2
-
113
-
-
0345724883
-
Evolutionary optimization, backpropagation, and data preparation issues in QSAR modeling of HIV inhibition by HEPT derivatives
-
Weekes, D.; Fogel, G.B. Evolutionary optimization, backpropagation, and data preparation issues in QSAR modeling of HIV inhibition by HEPT derivatives. Biosystems, 2003, 72, 149-158.
-
(2003)
Biosystems
, vol.72
, pp. 149-158
-
-
Weekes, D.1
Fogel, G.B.2
-
114
-
-
2942538155
-
Modelling blood-brain barrier partitioning using Bayesian neural nets
-
Winkler, D.A.; Burden, F.R. Modelling blood-brain barrier partitioning using Bayesian neural nets. J. Mol. Graph. Model., 2004, 22, 499-505.
-
(2004)
J. Mol. Graph. Model
, vol.22
, pp. 499-505
-
-
Winkler, D.A.1
Burden, F.R.2
-
115
-
-
14944350238
-
A general method for exploiting QSAR models in lead optimization
-
Lewis, R.A. A general method for exploiting QSAR models in lead optimization. J. Med. Chem. 2005, 48, 1638-1648.
-
(2005)
J. Med. Chem
, vol.48
, pp. 1638-1648
-
-
Lewis, R.A.1
-
116
-
-
33750321101
-
Novel approaches for small biomolecule classification and structural similarity search
-
Karakoc, E.; Sahinalp, S.C.; Cherkasov, A. Novel approaches for small biomolecule classification and structural similarity search. J. Chem. Inf. Model., 2006, 46, 2167-2182.
-
(2006)
J. Chem. Inf. Model
, vol.46
, pp. 2167-2182
-
-
Karakoc, E.1
Sahinalp, S.C.2
Cherkasov, A.3
-
117
-
-
0023751431
-
Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins
-
Cramer III, R.D.; 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
-
118
-
-
0027944195
-
Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity
-
Klebe, G.; Abraham, U.; Mietzner, T. Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J. Med. Chem., 1994, 37, 4130-4146.
-
(1994)
J. Med. Chem
, vol.37
, pp. 4130-4146
-
-
Klebe, G.1
Abraham, U.2
Mietzner, T.3
-
119
-
-
51249194645
-
A logical calculus of the ideas immanent in nervous activity
-
McCulloch, W.S., Pitts, W. A logical calculus of the ideas immanent in nervous activity. Bull. Math Biophys., 1943, 5, 115-133.
-
(1943)
Bull. Math Biophys
, vol.5
, pp. 115-133
-
-
McCulloch, W.S.1
Pitts, W.2
-
123
-
-
34248666540
-
Fuzzy sets
-
Zadeh, L.A. Fuzzy sets. Inform. Control, 1965, 8, 338-53.
-
(1965)
Inform. Control
, vol.8
, pp. 338-353
-
-
Zadeh, L.A.1
-
124
-
-
49949129142
-
Fuzzy Algorithms
-
Zadeh L.A. Fuzzy Algorithms. Inform. Control, 1968, 12, 94-102.
-
(1968)
Inform. Control
, vol.12
, pp. 94-102
-
-
Zadeh, L.A.1
-
125
-
-
33646361042
-
Fuzzy logic in medicine and bioinformatics
-
Torres, A.; Nieto, J.J. Fuzzy logic in medicine and bioinformatics. J.Biomed. Biotechnol., 2006, 2, 91908.
-
(2006)
J.Biomed. Biotechnol
, vol.2
, pp. 91908
-
-
Torres, A.1
Nieto, J.J.2
-
126
-
-
0038215370
-
-
Secaucus, NJ: Springer-Verlag New York, Inc
-
Mordeson, J.N.; Malik, D.S.; Cheng, S.-C. Fuzzy mathematics in medicine, Secaucus, NJ: Springer-Verlag New York, Inc., 2000.
-
(2000)
Fuzzy mathematics in medicine
-
-
Mordeson, J.N.1
Malik, D.S.2
Cheng, S.-C.3
-
127
-
-
0004259914
-
-
Berlin: Physica-Verlag, Berlin
-
Szczepaniak, P.S.; Lisoba, P.J.G.; Kacprzyk, J. Fuzzy systems in medicine, Berlin: Physica-Verlag, Berlin, 2000.
-
(2000)
Fuzzy systems in medicine
-
-
Szczepaniak, P.S.1
Lisoba, P.J.G.2
Kacprzyk, J.3
-
129
-
-
0003509518
-
-
Ruspini, E.H, Bonissone, P.P, Pedrycz, W. Eds, Bristol, UK: Oxford University Press
-
Ruspini, E.H.; Bonissone, P.P.; Pedrycz, W. Eds.; Handbook of fuzzy computation; Bristol, UK: Oxford University Press, 1998.
-
(1998)
Handbook of fuzzy computation
-
-
-
130
-
-
34248152046
-
Type-2 Fuzzy sets and systems: An overview
-
Mendel, J.M. Type-2 Fuzzy sets and systems: An overview. IEEE Comput. Intell. Mag., 2007, 2, 20-29.
-
(2007)
IEEE Comput. Intell. Mag
, vol.2
, pp. 20-29
-
-
Mendel, J.M.1
-
132
-
-
0016458950
-
The concept of a linguistic variable and its application to approximate reasoning-1
-
Zadeh, L.A. The concept of a linguistic variable and its application to approximate reasoning-1. Inform. Sci., 1975, 8, 199-249.
-
(1975)
Inform. Sci
, vol.8
, pp. 199-249
-
-
Zadeh, L.A.1
-
133
-
-
15344339772
-
A neuro-fuzzy approach to virtual screening in molecular bioinformatics
-
Paetz, J.; Schneider, G. A neuro-fuzzy approach to virtual screening in molecular bioinformatics. Fuzzy Sets Sys., 2005, 152, 67-82.
-
(2005)
Fuzzy Sets Sys
, vol.152
, pp. 67-82
-
-
Paetz, J.1
Schneider, G.2
-
134
-
-
0037424605
-
Efficient conformational sampling of local side-chain flexibility
-
Källblad, P.; Dean, P.M. Efficient conformational sampling of local side-chain flexibility. J. Mol. Biol., 2003, 326, 1651-1665.
-
(2003)
J. Mol. Biol
, vol.326
, pp. 1651-1665
-
-
Källblad, P.1
Dean, P.M.2
-
135
-
-
34248328283
-
Robust fuzzy mappings for QSAR studies
-
Kumar, M.; Thurow, K.; Stoll, N.; Stoll, R. Robust fuzzy mappings for QSAR studies. Eur. J. Med. Chem., 2007, 42, 675-685.
-
(2007)
Eur. J. Med. Chem
, vol.42
, pp. 675-685
-
-
Kumar, M.1
Thurow, K.2
Stoll, N.3
Stoll, R.4
-
136
-
-
0003806013
-
-
Wiley: New York, NY
-
Fogel, L.J.; Owens, A.; Walsh, M.J. Artificial intelligence through simulated evolution, Wiley: New York, NY, 1966.
-
(1966)
Artificial intelligence through simulated evolution
-
-
Fogel, L.J.1
Owens, A.2
Walsh, M.J.3
-
138
-
-
65749089166
-
-
Bremmerman, H.J. Optimization through evolution and recombination; Yovits M.C.; Jacobi G.T.; Goldstein G.D. Eds.; Self-organizing systems. Washington DC: Spartan Press, 1962.
-
Bremmerman, H.J. Optimization through evolution and recombination; Yovits M.C.; Jacobi G.T.; Goldstein G.D. Eds.; Self-organizing systems. Washington DC: Spartan Press, 1962.
-
-
-
-
142
-
-
0004222346
-
-
San Francisco, CA: Morgan Kaufmann
-
Eberhart, R.C.; Shi, Y.; Kennedy, J. Swarm intelligence, San Francisco, CA: Morgan Kaufmann, 2001.
-
(2001)
Swarm intelligence
-
-
Eberhart, R.C.1
Shi, Y.2
Kennedy, J.3
-
143
-
-
0031122887
-
-
Dorigo, M; Gambardella, L.M. Ant colony system: A cooperative learning approach to the traveling salesman problem. IEEE Trans. Evol. Comput., 1997, 1, 53-66.
-
Dorigo, M; Gambardella, L.M. Ant colony system: A cooperative learning approach to the traveling salesman problem. IEEE Trans. Evol. Comput., 1997, 1, 53-66.
-
-
-
-
144
-
-
0003853519
-
Differential evolution: A simple and efficient sdaptive scheme for global optimization over continuous spaces
-
Technical report TR-95-012, ICSI, March
-
Storn, R.; Price, K. Differential evolution: A simple and efficient sdaptive scheme for global optimization over continuous spaces. Technical report TR-95-012, ICSI, March 1995.
-
(1995)
-
-
Storn, R.1
Price, K.2
-
145
-
-
0033115654
-
System design by constraint adaptation and differential evolution
-
Storn, R. System design by constraint adaptation and differential evolution. IEEE Trans. Evol. Comput., 1999, 3, 22-34.
-
(1999)
IEEE Trans. Evol. Comput
, vol.3
, pp. 22-34
-
-
Storn, R.1
-
147
-
-
0025107328
-
Evolving neural networks
-
Fogel, D.B.; Fogel, L.J.; Porto, V.W. Evolving neural networks. Biol. Cybern., 1990, 63, 487-93.
-
(1990)
Biol. Cybern
, vol.63
, pp. 487-493
-
-
Fogel, D.B.1
Fogel, L.J.2
Porto, V.W.3
-
148
-
-
0033362601
-
Evolving artificial neural networks
-
Yao, X. Evolving artificial neural networks. Proc. IEEE, 1999, 87, 1423-1447.
-
(1999)
Proc. IEEE
, vol.87
, pp. 1423-1447
-
-
Yao, X.1
-
149
-
-
65749111584
-
Evolved Neural Networks for High Throughput Anti-HIV Ligand Screening
-
Vancouver, Canada
-
MA, C.Y.C.; Wong, S.W.M.; Hecht, D.; Fogel, G.B. Evolved Neural Networks for High Throughput Anti-HIV Ligand Screening. IEEE Congress on Evolutionary Computation, Vancouver, Canada, 2006, 9284-9291.
-
(2006)
IEEE Congress on Evolutionary Computation
, pp. 9284-9291
-
-
MA, C.Y.C.1
Wong, S.W.M.2
Hecht, D.3
Fogel, G.B.4
-
150
-
-
34547963127
-
High-throughput ligand screening via pre-clustering and rvolved neural networks. IEEE/ACM Trans
-
Hecht, D.; Fogel, G.B. High-throughput ligand screening via pre-clustering and rvolved neural networks. IEEE/ACM Trans. Comput. Biol. Bioinf., 2007, 4, 476-84.
-
(2007)
Comput. Biol. Bioinf
, vol.4
, pp. 476-484
-
-
Hecht, D.1
Fogel, G.B.2
-
151
-
-
39949084319
-
QSAR using evolved neural networks for the inhibition of mutant PfDHFR by pyrimethamine derivatives
-
Hecht, D.; Cheung, M.; Fogel, G.B. QSAR using evolved neural networks for the inhibition of mutant PfDHFR by pyrimethamine derivatives. Biosystems 2008, 92, 10-15.
-
(2008)
Biosystems
, vol.92
, pp. 10-15
-
-
Hecht, D.1
Cheung, M.2
Fogel, G.B.3
-
152
-
-
55749084035
-
-
San Diego, CA
-
Cheung, M.; Johnson, S.; Hecht, D.; Fogel, G.B. Quantitative structure-property relationships for drug solubility prediction using evolved neural networks; Natural Selection, Inc.: San Diego, CA, 2008; pp. 688-693.
-
(2008)
Quantitative structure-property relationships for drug solubility prediction using evolved neural networks; Natural Selection, Inc
, pp. 688-693
-
-
Cheung, M.1
Johnson, S.2
Hecht, D.3
Fogel, G.B.4
-
153
-
-
0344254815
-
Drug discovery using support vector machines. The case studies of drug-likeness, agrochemical-likeness, and enzyme inhibition predictions
-
Zernov, V.V.; Balakin, K.V.; Ivaschenko, A.A.; Nikolay P.; Savchuk, N.P.; Pletnev, I.V. Drug discovery using support vector machines. The case studies of drug-likeness, agrochemical-likeness, and enzyme inhibition predictions. J. Chem. Inf. Comput. Sci., 2003, 43, 2048-2056.
-
(2003)
J. Chem. Inf. Comput. Sci
, vol.43
, pp. 2048-2056
-
-
Zernov, V.V.1
Balakin, K.V.2
Ivaschenko, A.A.3
Nikolay, P.4
Savchuk, N.P.5
Pletnev, I.V.6
-
154
-
-
43049157546
-
A support vector machines approach for virtual screening of active compounds of single and multiple mechanisms from large libraries at an improved hit-rate and enrichment factor
-
Han, L.Y.; Ma, X.H.; Lin, H.H.; Jia, J.; Zhu, F.; Xuec, Y.; Li, Z.R.; Cao, Z.W.; Ji, Z.L.; Chen, Y.Z. A support vector machines approach for virtual screening of active compounds of single and multiple mechanisms from large libraries at an improved hit-rate and enrichment factor. J. Mol. Graph. Model., 2008, 26, 1276-1286.
-
(2008)
J. Mol. Graph. Model
, vol.26
, pp. 1276-1286
-
-
Han, L.Y.1
Ma, X.H.2
Lin, H.H.3
Jia, J.4
Zhu, F.5
Xuec, Y.6
Li, Z.R.7
Cao, Z.W.8
Ji, Z.L.9
Chen, Y.Z.10
-
155
-
-
39749108754
-
Efficient comprehensive scoring of docked protein complexes using probabilistic support vector machines
-
Martin, O.; Schomburg, D. Efficient comprehensive scoring of docked protein complexes using probabilistic support vector machines. Proteins, 2008, 70, 1367-1378.
-
(2008)
Proteins
, vol.70
, pp. 1367-1378
-
-
Martin, O.1
Schomburg, D.2
-
157
-
-
17644371944
-
A support vector machine approach to the identification of phosphorylation sites
-
Plewczynski, D.; Tkacz, A.;Godzik, A.;Rychlewski, L. A support vector machine approach to the identification of phosphorylation sites. Cell. Mol. Biol. Lett., 2005, 10, 73-89.
-
(2005)
Cell. Mol. Biol. Lett
, vol.10
, pp. 73-89
-
-
Plewczynski, D.1
Tkacz, A.2
Godzik, A.3
Rychlewski, L.4
-
158
-
-
0000667930
-
Training nu-support vector classifiers: Theory and algorithms
-
Chang, C.C.; Lin, C.J. Training nu-support vector classifiers: Theory and algorithms. Neural Comput., 2001, 13, 2119-2147.
-
(2001)
Neural Comput
, vol.13
, pp. 2119-2147
-
-
Chang, C.C.1
Lin, C.J.2
-
159
-
-
4143132047
-
Combination of a naive Bayes classifier with consensus scoring improves enrichment of high-throughput docking results
-
Klon, A.E.; Glick, M.; Davies, J.W. Combination of a naive Bayes classifier with consensus scoring improves enrichment of high-throughput docking results. J. Med. Chem., 2004, 47, 4356-4359.
-
(2004)
J. Med. Chem
, vol.47
, pp. 4356-4359
-
-
Klon, A.E.1
Glick, M.2
Davies, J.W.3
-
160
-
-
2442716437
-
Finding more needles in the haystack: A simple and efficient method for improving high-throughput docking results
-
Klon, A.E.; Glick, M.; Thoma, M.; Acklin, P.; Davies, J.W. Finding more needles in the haystack: A simple and efficient method for improving high-throughput docking results. J. Med. Chem., 2004, 47, 2743.
-
(2004)
J. Med. Chem
, vol.47
, pp. 2743
-
-
Klon, A.E.1
Glick, M.2
Thoma, M.3
Acklin, P.4
Davies, J.W.5
-
161
-
-
27444445346
-
PostDock A structural, empirical approach to scoring protein ligand complexes
-
Springer, C.; Adalsteinsson, H.; Young, M.M.; Kegelmeyer, P.W. Roe, D.C. PostDock A structural, empirical approach to scoring protein ligand complexes. J. Med. Chem., 2005, 48, 6821-6831.
-
(2005)
J. Med. Chem
, vol.48
, pp. 6821-6831
-
-
Springer, C.1
Adalsteinsson, H.2
Young, M.M.3
Kegelmeyer, P.W.4
Roe, D.C.5
-
162
-
-
2942704292
-
Novel scoring functions comprising QXP, SASA, and protein side-chain entropy terms
-
Giordanetto, F.; Cotesta, S.; Catana, C.; Trosset, J.Y.; Vulpetti, A.; Stouten, P.F.W.; Kroemer, R.T. Novel scoring functions comprising QXP, SASA, and protein side-chain entropy terms. J. Chem. Inf. Comput. Sci., 2004, 44, 882-893.
-
(2004)
J. Chem. Inf. Comput. Sci
, vol.44
, pp. 882-893
-
-
Giordanetto, F.1
Cotesta, S.2
Catana, C.3
Trosset, J.Y.4
Vulpetti, A.5
Stouten, P.F.W.6
Kroemer, R.T.7
-
163
-
-
42449142325
-
A new approach to rapid scoring functions that uses a MD-averaged potential energy grid and a solvent-accessible surface area term with parameters GA fit to experimental data
-
Pearlman, D.A.; Rao, B.G.; Charifson, P. FURSMASA: A new approach to rapid scoring functions that uses a MD-averaged potential energy grid and a solvent-accessible surface area term with parameters GA fit to experimental data. Proteins, 2008, 71, 1519-1538.
-
(2008)
Proteins
, vol.71
, pp. 1519-1538
-
-
Pearlman, D.A.1
Rao, B.G.2
Charifson3
FURSMASA, P.4
-
164
-
-
6044238257
-
A docking score function for estimating ligand-protein interactions: Application to acetylcholinesterase inhibition
-
Guo, J.; Hurley, M.M.; Wright, J.B.; Gerald H. Lushington, G.H. A docking score function for estimating ligand-protein interactions: application to acetylcholinesterase inhibition. J. Med. Chem., 2004, 47, 5492-5500.
-
(2004)
J. Med. Chem
, vol.47
, pp. 5492-5500
-
-
Guo, J.1
Hurley, M.M.2
Wright, J.B.3
Gerald, H.4
Lushington, G.H.5
-
165
-
-
33846889763
-
Novel, customizable scoring functions, parameterized using N-PLS, for structure-based drug discovery
-
Catana, C.; Pieter, F.W.; Stouten, P.F.W. Novel, customizable scoring functions, parameterized using N-PLS, for structure-based drug discovery. J. Chem. Inf. Model., 2007, 47, 85-91.
-
(2007)
J. Chem. Inf. Model
, vol.47
, pp. 85-91
-
-
Catana, C.1
Pieter, F.W.2
Stouten, P.F.W.3
-
166
-
-
41549086249
-
Supervised scoring models with docked ligand conformations for structure-based virtual screening
-
Teramoto, R.; Fukunishi, H. Supervised scoring models with docked ligand conformations for structure-based virtual screening. J. Chem. Inf. Model., 2008, 48, 288-295.
-
(2008)
J. Chem. Inf. Model
, vol.48
, pp. 288-295
-
-
Teramoto, R.1
Fukunishi, H.2
-
167
-
-
2942721004
-
Virtual screening using protein-ligand docking: Avoiding artificial enrichment
-
Verdonk, M.L.; Berdini, V.; Hartshorn, M.J.; Mooij, W.T.M.; Murray, C.W.; Taylor, R.D.; Watson, P. Virtual screening using protein-ligand docking: Avoiding artificial enrichment. J. Chem. Inf. Comput. Sci., 2004, 44, 793.
-
(2004)
J. Chem. Inf. Comput. Sci
, vol.44
, pp. 793
-
-
Verdonk, M.L.1
Berdini, V.2
Hartshorn, M.J.3
Mooij, W.T.M.4
Murray, C.W.5
Taylor, R.D.6
Watson, P.7
-
168
-
-
26944456622
-
Knowledge-driven lead discovery
-
Pirard, B. Knowledge-driven lead discovery. Mini Rev. Med. Chem., 2005, 5, 1045-1052.
-
(2005)
Mini Rev. Med. Chem
, vol.5
, pp. 1045-1052
-
-
Pirard, B.1
-
169
-
-
0037011890
-
Development of a virtual screening method for identification of "frequent hitters" in compound libraries
-
Roche, O.; Schneider, P.; Zuegge, J.; Guba, W.; Kansy, M.; Alanine, A.; Bleicher, K.; Danel, F.; Gutknecht, E.-M.; Rogers-Evans, M.; Neidhart, W.; Stadler, H.; Dillon, M.; Sjögren, E.; Foutouhi, N.; Gillespie, P.; Goodnow, R.; Harris, W.; Jones, P.; Taniguchi, M.; Tsujii, S.; von der Saal, W.; Zimmermann, G.; Schneider, G. Development of a virtual screening method for identification of "frequent hitters" in compound libraries. J. Med. Chem., 2002, 45, 137-142.
-
(2002)
J. Med. Chem
, vol.45
, pp. 137-142
-
-
Roche, O.1
Schneider, P.2
Zuegge, J.3
Guba, W.4
Kansy, M.5
Alanine, A.6
Bleicher, K.7
Danel, F.8
Gutknecht, E.-M.9
Rogers-Evans, M.10
Neidhart, W.11
Stadler, H.12
Dillon, M.13
Sjögren, E.14
Foutouhi, N.15
Gillespie, P.16
Goodnow, R.17
Harris, W.18
Jones, P.19
Taniguchi, M.20
Tsujii, S.21
von der Saal, W.22
Zimmermann, G.23
Schneider, G.24
more..
-
170
-
-
0346962971
-
Structural interaction fingerprint (SIFt): A novel method for analyzing three-dimensional protein-ligand binding interactions
-
Deng, Z.; Chuaqui, C.; Singh, J. Structural interaction fingerprint (SIFt): A novel method for analyzing three-dimensional protein-ligand binding interactions. J. Med. Chem., 2004, 47, 337-344.
-
(2004)
J. Med. Chem
, vol.47
, pp. 337-344
-
-
Deng, Z.1
Chuaqui, C.2
Singh, J.3
-
171
-
-
12144249613
-
Interaction profiles of protein kinase-inhibitor complexes and their application to virtual screening
-
Chuaqui, C.; Deng, Z.; Singh, J. Interaction profiles of protein kinase-inhibitor complexes and their application to virtual screening. J. Med. Chem., 2005, 48, 121-133.
-
(2005)
J. Med. Chem
, vol.48
, pp. 121-133
-
-
Chuaqui, C.1
Deng, Z.2
Singh, J.3
-
172
-
-
0037153231
-
Molecular docking and 3D-QSAR studies on gag peptide analogue inhibitors interacting with human cyclophilin A
-
Cui, M.; Huang, X.; Luo, X.; Briggs, J.M.; Ji, R.; Chen, K.; Shen, J.; Jiang, H. Molecular docking and 3D-QSAR studies on gag peptide analogue inhibitors interacting with human cyclophilin A. J. Med. Chem., 2002, 45, 5249-5259.
-
(2002)
J. Med. Chem
, vol.45
, pp. 5249-5259
-
-
Cui, M.1
Huang, X.2
Luo, X.3
Briggs, J.M.4
Ji, R.5
Chen, K.6
Shen, J.7
Jiang, H.8
-
173
-
-
0037168053
-
Inhibitory mode of 1,5-diarylpyrazole derivatives against cyclooxygenase-2 and cyclooxygenase-1: Molecular docking and 3D QSAR analyses
-
Liu, H.; Huang, X.; Shen, J.; Luo, X.; Li, M.; Xiong, B.; Chen, G.; Shen, J.; Yang, Y.; Jiang, H.; Chen, K. Inhibitory mode of 1,5-diarylpyrazole derivatives against cyclooxygenase-2 and cyclooxygenase-1: Molecular docking and 3D QSAR analyses. J. Med. Chem., 2002, 45, 4816-4827.
-
(2002)
J. Med. Chem
, vol.45
, pp. 4816-4827
-
-
Liu, H.1
Huang, X.2
Shen, J.3
Luo, X.4
Li, M.5
Xiong, B.6
Chen, G.7
Shen, J.8
Yang, Y.9
Jiang, H.10
Chen, K.11
-
174
-
-
3042747902
-
Inhibitory mode of indole-2-carboxamide derivatives against HLGPa: Molecular docking and 3D-QSAR analyses
-
Liu, G.; Zhang, Z.; Luo, X.; Shen, J.; Liu, H.; Shen, X.; Chen, K.; Jiang, H. Inhibitory mode of indole-2-carboxamide derivatives against HLGPa: Molecular docking and 3D-QSAR analyses. Bioorg. Med. Chem., 2004, 12, 4147-4157.
-
(2004)
Bioorg. Med. Chem
, vol.12
, pp. 4147-4157
-
-
Liu, G.1
Zhang, Z.2
Luo, X.3
Shen, J.4
Liu, H.5
Shen, X.6
Chen, K.7
Jiang, H.8
-
175
-
-
26944484425
-
Modeling ligand-receptor interaction for some MHC class II HLA-DR4 peptide mimetic inhibitors using several molecular docking and 3D QSAR techniques
-
Wei, H.-Y.; Tsai, K.-C.; Lin, T.-H. Modeling ligand-receptor interaction for some MHC class II HLA-DR4 peptide mimetic inhibitors using several molecular docking and 3D QSAR techniques. J. Chem. Inf. Model., 2005, 45, 1343-1351.
-
(2005)
J. Chem. Inf. Model
, vol.45
, pp. 1343-1351
-
-
Wei, H.-Y.1
Tsai, K.-C.2
Lin, T.-H.3
-
176
-
-
13844312018
-
Molecular docking and 3D-QSAR studies on the binding mechanism of statine-based peptidomimetics with β-secretase
-
Zuo, Z.; Luo, X.; Zhu, W.; Shen, J.; Shen, X.; Jiang, H.; Chen, K. Molecular docking and 3D-QSAR studies on the binding mechanism of statine-based peptidomimetics with β-secretase. Bioorg. Med. Chem., 2005, 13, 2121-2131.
-
(2005)
Bioorg. Med. Chem
, vol.13
, pp. 2121-2131
-
-
Zuo, Z.1
Luo, X.2
Zhu, W.3
Shen, J.4
Shen, X.5
Jiang, H.6
Chen, K.7
-
177
-
-
33644750237
-
3D-QSAR and docking studies of aldehyde inhibitors of human cathepsin K
-
Pan, X.; Tan, N.; Zeng, G.; Huang, H. 3D-QSAR and docking studies of aldehyde inhibitors of human cathepsin K. Bioorg. Med. Chem., 2006, 14, 2771-2778.
-
(2006)
Bioorg. Med. Chem
, vol.14
, pp. 2771-2778
-
-
Pan, X.1
Tan, N.2
Zeng, G.3
Huang, H.4
-
178
-
-
33746924874
-
Exploration of a binding mode of benzothiazol-2-yl acetonitrile pyrimidine core based derivatives as potent c-Jun N-terminal kinase-3 inhibitors and 3D-QSAR analyses
-
Sharma, P.; Ghoshal, N. Exploration of a binding mode of benzothiazol-2-yl acetonitrile pyrimidine core based derivatives as potent c-Jun N-terminal kinase-3 inhibitors and 3D-QSAR analyses. J. Chem. Inf. Model., 2006, 46, 1763-1774.
-
(2006)
J. Chem. Inf. Model
, vol.46
, pp. 1763-1774
-
-
Sharma, P.1
Ghoshal, N.2
-
179
-
-
33846872804
-
Interpretation of scoring functions using 3D molecular fields. mapping the diacylhydrazine-binding pocket of an insect ecdysone receptor
-
Bordas, B.; Belai, I.; Lopata, A.; Szanto, Z. Interpretation of scoring functions using 3D molecular fields. mapping the diacylhydrazine-binding pocket of an insect ecdysone receptor. J. Chem. Inf. Model., 2007, 47, 176-185.
-
(2007)
J. Chem. Inf. Model
, vol.47
, pp. 176-185
-
-
Bordas, B.1
Belai, I.2
Lopata, A.3
Szanto, Z.4
-
180
-
-
35248826518
-
Design of inhibitors of the MurF enzyme of Streptococcus pneumoniae using docking, 3DQSAR, and de Novo design
-
Khedkar, S.A.; Malde, A.K.; Coutinho, E.C. Design of inhibitors of the MurF enzyme of Streptococcus pneumoniae using docking, 3DQSAR, and de Novo design. J. Chem. Inf. Model., 2007, 47, 1839-1846.
-
(2007)
J. Chem. Inf. Model
, vol.47
, pp. 1839-1846
-
-
Khedkar, S.A.1
Malde, A.K.2
Coutinho, E.C.3
-
181
-
-
56849085011
-
An efficient tool for identifying inhibitors based on 3D-QSAR and docking using feature-shape pharmacophore of biologically active conformation - A case study with CDK2/CyclinA
-
doi:10.1016/ j.ejmech.2007.10.016
-
Mascarenhas, N.M.; Ghoshal, N. An efficient tool for identifying inhibitors based on 3D-QSAR and docking using feature-shape pharmacophore of biologically active conformation - A case study with CDK2/CyclinA. Eur. J. Med. Chem., 2007, - doi:10.1016/ j.ejmech.2007.10.016.
-
(2007)
Eur. J. Med. Chem
-
-
Mascarenhas, N.M.1
Ghoshal, N.2
-
182
-
-
40049109337
-
3D-QSAR and docking studies of aminopyridine carboxamide inhibitors of c-Jun N-terminal kinase-1
-
Yi, P.; Qiu, M. 3D-QSAR and docking studies of aminopyridine carboxamide inhibitors of c-Jun N-terminal kinase-1. Eur. J. Med. Chem., 2008, 43, 604-613.
-
(2008)
Eur. J. Med. Chem
, vol.43
, pp. 604-613
-
-
Yi, P.1
Qiu, M.2
-
183
-
-
45749088639
-
-
Zaheer-ul-Haq; Uddin, R.; Yuan, H.; Pavel A.; Petukhov, P.A.; Choudhary, M. I.; Madura, J.D. Receptor-based modeling and 3DQSAR for a quantitative production of the butyrylcholinesterase inhibitors based on genetic algorithm. J. Chem. Inf. Model., 2008, 48, 1092-1103.
-
Zaheer-ul-Haq; Uddin, R.; Yuan, H.; Pavel A.; Petukhov, P.A.; Choudhary, M. I.; Madura, J.D. Receptor-based modeling and 3DQSAR for a quantitative production of the butyrylcholinesterase inhibitors based on genetic algorithm. J. Chem. Inf. Model., 2008, 48, 1092-1103.
-
-
-
-
184
-
-
41149096934
-
Structural features of diverse ligands influencing binding affinities to estrogen and estrogen β receptors. Part II. Molecular descriptors calculated from conformation of the ligands in the complex resulting from previous docking study
-
Spreafico, M.; Boriani, E.; Benfenati, E.; Novic, M. Structural features of diverse ligands influencing binding affinities to estrogen and estrogen β receptors. Part II. Molecular descriptors calculated from conformation of the ligands in the complex resulting from previous docking study. Mol. Divers., 2007, 11, 171-181.
-
(2007)
Mol. Divers
, vol.11
, pp. 171-181
-
-
Spreafico, M.1
Boriani, E.2
Benfenati, E.3
Novic, M.4
-
185
-
-
38849197951
-
Discovery of new MurF inhibitors via pharmacophore modeling and QSAR analysis followed by in silico screening
-
Taha, M.O.; Atallah, N.; Al-Bakri, A.G.; Paradis-Bleau, C.; Zalloum, H.; Younis, K.S.; Levesque, R.C. Discovery of new MurF inhibitors via pharmacophore modeling and QSAR analysis followed by in silico screening. Bioor. Med. Chem., 2008, 16, 1218-1235.
-
(2008)
Bioor. Med. Chem
, vol.16
, pp. 1218-1235
-
-
Taha, M.O.1
Atallah, N.2
Al-Bakri, A.G.3
Paradis-Bleau, C.4
Zalloum, H.5
Younis, K.S.6
Levesque, R.C.7
-
186
-
-
20144366000
-
Focused combinatorial library design based on structural diversity, drug-likeness and binding affinity score
-
Chen, G.; Zheng, S.; Luo, X.; Shen, J.; Zhu, W.; Liu, H.; Gui, C.; Zhang, J.; Zheng, M.; Puah, C.M.; Chen, K.; Jiang, H. Focused combinatorial library design based on structural diversity, drug-likeness and binding affinity score. J. Comb. Chem., 2005, 7, 398-406.
-
(2005)
J. Comb. Chem
, vol.7
, pp. 398-406
-
-
Chen, G.1
Zheng, S.2
Luo, X.3
Shen, J.4
Zhu, W.5
Liu, H.6
Gui, C.7
Zhang, J.8
Zheng, M.9
Puah, C.M.10
Chen, K.11
Jiang, H.12
-
187
-
-
34347220502
-
Complex-type-dependent scoring functions in protein-protein docking
-
Li, C.H.; Ma, X.H.; Shen, L.Z.; Shan Chang, S.; Chen, W.Z.; Wang, C.X. Complex-type-dependent scoring functions in protein-protein docking. Biophys. Chem., 2007, 129, 1-10.
-
(2007)
Biophys. Chem
, vol.129
, pp. 1-10
-
-
Li, C.H.1
Ma, X.H.2
Shen, L.Z.3
Shan Chang, S.4
Chen, W.Z.5
Wang, C.X.6
-
188
-
-
44449170479
-
-
Sullivan, D.C; Martin, E.J. ChemInform abstract: Rxploiting structure -
-
Sullivan, D.C; Martin, E.J. ChemInform abstract: Rxploiting structure - activity relationships in docking. J. Chem. Inf. Model., 2008, 48, 817-830.
-
-
-
-
189
-
-
0029000922
-
Prediction of drug binding affinities by comparative binding energy analysis
-
Ortiz, A.R.; Pisabarro, M.T.; Gago, F.; Wade, R.C. Prediction of drug binding affinities by comparative binding energy analysis. J. Med. Chem., 1995, 38, 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
-
190
-
-
0035866695
-
Comparative binding energy (COMBINE) analysis of influenza neuraminidase-inhibitor complexes
-
Wang, T.; Wade, R.C. Comparative binding energy (COMBINE) analysis of influenza neuraminidase-inhibitor complexes. J. Med. Chem., 2001, 44, 961-971.
-
(2001)
J. Med. Chem
, vol.44
, pp. 961-971
-
-
Wang, T.1
Wade, R.C.2
-
191
-
-
0842304437
-
Virtual screening with flexible docking and COMBINE-based models. application to a series of factor Xa inhibitors
-
Murcia, M.; Ortiz, A.R. Virtual screening with flexible docking and COMBINE-based models. application to a series of factor Xa inhibitors. J. Med. Chem., 2004, 47, 805-820.
-
(2004)
J. Med. Chem
, vol.47
, pp. 805-820
-
-
Murcia, M.1
Ortiz, A.R.2
-
192
-
-
26944499806
-
-
Antes, I.; Merkwirth, C.; Lengauer, T. POEM: Parameter optimization using ensemble methods: Application to target specific scoring functions. J. Chem. Inf. Model., 2005, 45, 1291-1302.
-
Antes, I.; Merkwirth, C.; Lengauer, T. POEM: Parameter optimization using ensemble methods: Application to target specific scoring functions. J. Chem. Inf. Model., 2005, 45, 1291-1302.
-
-
-
-
193
-
-
0031138166
-
The deceptor-like neural network for modeling corticosteroid and testosterone binding globulins
-
Polański, J. The deceptor-like neural network for modeling corticosteroid and testosterone binding globulins. J. Chem. Inf. Comput. Sci., 1997, 37, 553-561.
-
(1997)
J. Chem. Inf. Comput. Sci
, vol.37
, pp. 553-561
-
-
Polański, J.1
-
194
-
-
33845772311
-
Synergistic use of compound properties and docking scores in neural network modeling of CYP2D6 binding: Predicting affinity and conformational sampling
-
Bazeley, P.S.; Prithivi, S.; Struble, C.A.; Povinelli, R.J.; Sem, D.S. Synergistic use of compound properties and docking scores in neural network modeling of CYP2D6 binding: Predicting affinity and conformational sampling. J. Chem. Inf. Model., 2006, 46, 2698-2708.
-
(2006)
J. Chem. Inf. Model
, vol.46
, pp. 2698-2708
-
-
Bazeley, P.S.1
Prithivi, S.2
Struble, C.A.3
Povinelli, R.J.4
Sem, D.S.5
-
195
-
-
34047129815
-
A new protein-protein docking scoring function based on interface residue properties
-
Bernauer, J.; Aze', J.; Janin, J.; Poupon, A. A new protein-protein docking scoring function based on interface residue properties. Bionformatics, 2007, 23, 555-562.
-
(2007)
Bionformatics
, vol.23
, pp. 555-562
-
-
Bernauer, J.1
Aze', J.2
Janin, J.3
Poupon, A.4
-
196
-
-
1842535990
-
Classification Analysis of P-glycoprotein substrate specificity
-
Didziapetris, R.; Japertas, P.; Avdeef, A.; Petrauskas, A. Classification Analysis of P-glycoprotein substrate specificity. J. Drug Target., 2003, 11, 391-406.
-
(2003)
J. Drug Target
, vol.11
, pp. 391-406
-
-
Didziapetris, R.1
Japertas, P.2
Avdeef, A.3
Petrauskas, A.4
-
197
-
-
4444275159
-
Fuzzy pharmacophore models from molecular alignments for correlation-vector-based virtual screening
-
Renner, S.; Schneider, G. Fuzzy pharmacophore models from molecular alignments for correlation-vector-based virtual screening. J. Med. Chem., 2004, 47, 4653-4664.
-
(2004)
J. Med. Chem
, vol.47
, pp. 4653-4664
-
-
Renner, S.1
Schneider, G.2
-
198
-
-
40949126936
-
A genetic algorithm optimized fuzzy neural network analysis of the affinity of inhibitors for HIV-1 protease
-
Fabry-Asztalos, L.; Andonie, R.; Collar, C.J.; Abdul-Wahid, S.; Salim, N. A genetic algorithm optimized fuzzy neural network analysis of the affinity of inhibitors for HIV-1 protease. Bioorg. Med. Chem., 2008, 16, 2903-2911.
-
(2008)
Bioorg. Med. Chem
, vol.16
, pp. 2903-2911
-
-
Fabry-Asztalos, L.1
Andonie, R.2
Collar, C.J.3
Abdul-Wahid, S.4
Salim, N.5
-
199
-
-
23944499528
-
Improving binding mode predictions by docking into protein-specifically adapted potential fields
-
Radestock, S.; Bohm, M.; Gohlke, H. Improving binding mode predictions by docking into protein-specifically adapted potential fields. J. Med. Chem., 2005, 48, 5466-5479.
-
(2005)
J. Med. Chem
, vol.48
, pp. 5466-5479
-
-
Radestock, S.1
Bohm, M.2
Gohlke, H.3
-
200
-
-
26444468103
-
-
Mooij, W.T.M; Verdonk, M.L. General and targeted statistical potentials for protein-ligand interactions. Proteins: Struct. Func. Bioinf., 2005, 61, 272-287.
-
Mooij, W.T.M; Verdonk, M.L. General and targeted statistical potentials for protein-ligand interactions. Proteins: Struct. Func. Bioinf., 2005, 61, 272-287.
-
-
-
|