-
1
-
-
36749002607
-
A general approach for developing system-specific functions to score protein-ligand docked complexes using support vector inductive logic programming
-
Amini, A. et al. (2007) A general approach for developing system-specific functions to score protein-ligand docked complexes using support vector inductive logic programming. Proteins, 69, 823-831.
-
(2007)
Proteins
, vol.69
, pp. 823-831
-
-
Amini, A.1
-
2
-
-
0032533791
-
Flexible docking using Tabu search and an empirical estimate of binding affinity
-
Baxter, C.A. et al. (1998) Flexible docking using Tabu search and an empirical estimate of binding affinity. Proteins: Struct., Funct., Genet., 33, 367-382.
-
(1998)
Proteins: Struct., Funct., Genet.
, vol.33
, pp. 367-382
-
-
Baxter, C.A.1
-
3
-
-
0033954256
-
The Protein Data Bank
-
Berman, H.M. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
-
4
-
-
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. (1994) 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., 8, 243-256.
-
(1994)
J. Comput.-Aided Mol. Des.
, vol.8
, pp. 243-256
-
-
Böhm, H.-J.1
-
5
-
-
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. (1998) 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., 12, 309-323.
-
(1998)
J. Comput.-Aided Mol. Des.
, vol.12
, pp. 309-323
-
-
Böhm, H.-J.1
-
6
-
-
0035478854
-
Random Forests
-
Breiman, L. (2001) Random Forests. Mach. Learn., 45, 5-32.
-
(2001)
Mach. Learn.
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
8
-
-
67349205019
-
Achemogenomic approach to drug discovery: focus on cardiovascular diseases
-
Cases, M. and Mestres, J. (2009)Achemogenomic approach to drug discovery: focus on cardiovascular diseases. Drug Discov. Today, 14, 479-485.
-
(2009)
Drug Discov. Today
, vol.14
, pp. 479-485
-
-
Cases, M.1
Mestres, J.2
-
9
-
-
28944450149
-
Prediction of protein-protein interactions using random decision forest framework
-
Chen, X. and Liu, M. (2005) Prediction of protein-protein interactions using random decision forest framework. Bioinformatics, 21, 4394-4400.
-
(2005)
Bioinformatics
, vol.21
, pp. 4394-4400
-
-
Chen, X.1
Liu, M.2
-
10
-
-
66149103553
-
Comparative assessment of scoring functions on a diverse test set
-
Cheng, T. et al. (2009) Comparative assessment of scoring functions on a diverse test set. J. Chem. Inf. Model., 49, 1079-1093.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1079-1093
-
-
Cheng, T.1
-
11
-
-
1842740026
-
Predicting protein-ligand binding affinities using novel geometrical descriptors and machine-learning methods
-
Deng, W. et al. (2004) Predicting protein-ligand binding affinities using novel geometrical descriptors and machine-learning methods. J. Chem. Inf. Comput. Sci., 44, 699-703.
-
(2004)
J. Chem. Inf. Comput. Sci.
, vol.44
, pp. 699-703
-
-
Deng, W.1
-
12
-
-
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. et al. (1997) 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., 11, 425-445.
-
(1997)
J. Comput.-Aided Mol. Des.
, vol.11
, pp. 425-445
-
-
Eldridge, M.D.1
-
13
-
-
37449004656
-
Molecular docking for substrate identification: the short-chain dehydrogenases/reductases
-
Favia, A.D. et al. (2008) Molecular docking for substrate identification: the short-chain dehydrogenases/reductases. J. Mol. Biol., 375, 855-874.
-
(2008)
J. Mol. Biol.
, vol.375
, pp. 855-874
-
-
Favia, A.D.1
-
14
-
-
1942471391
-
Assessing scoring functions for protein-ligand interactions
-
Ferrara, P. et al. (2004) Assessing scoring functions for protein-ligand interactions. J. Med. Chem., 47, 3032-3047.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 3032-3047
-
-
Ferrara, P.1
-
15
-
-
12144289984
-
Glide: a new approach for rapid, accurate docking and scoring 1. Method and assessment of docking accuracy
-
Friesner, R.A. et al. (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem., 47, 1739-1749.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 1739-1749
-
-
Friesner, R.A.1
-
16
-
-
33750124980
-
Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes
-
Friesner, R.A. et al. (2006) Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J. Med. Chem., 49, 6177-6196.
-
(2006)
J. Med. Chem.
, vol.49
, pp. 6177-6196
-
-
Friesner, R.A.1
-
17
-
-
0029294584
-
Molecular recognition of the inhibitor AG-1343 by HIV-1 Protease: conformationally flexible docking by evolutionary programming
-
Gehlhaar, D.K. et al. (1995) Molecular recognition of the inhibitor AG-1343 by HIV-1 Protease: conformationally flexible docking by evolutionary programming. Chem. Biol., 2, 317-324.
-
(1995)
Chem. Biol.
, vol.2
, pp. 317-324
-
-
Gehlhaar, D.K.1
-
18
-
-
0034645763
-
Knowledge-based scoring function to predict protein-ligand interactions
-
Gohlke, H. et al. (2000) Knowledge-based scoring function to predict protein-ligand interactions. J. Mol. Biol., 295, 337-356.
-
(2000)
J. Mol. Biol.
, vol.295
, pp. 337-356
-
-
Gohlke, H.1
-
19
-
-
60349109713
-
Computational evaluation of protein-small molecule binding
-
Guvench, O. and MacKerell, A.D., Jr. (2009) Computational evaluation of protein-small molecule binding. Curr. Opin. Struct. Biol., 19, 56-61.
-
(2009)
Curr. Opin. Struct. Biol.
, vol.19
, pp. 56-61
-
-
Guvench, O.1
MacKerell A.D., Jr.2
-
20
-
-
62149135362
-
Prediction of glycosylation sites using random forests
-
Hamby, S.E.and Hirst, J.D. (2008) Prediction of glycosylation sites using random forests. BMC Bioinformatics, 9, 500.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 500
-
-
Hamby, S.E.1
Hirst, J.D.2
-
21
-
-
33750898990
-
Molecular mechanics methods for predicting protein-ligand binding
-
Huang, N. et al. (2006) Molecular mechanics methods for predicting protein-ligand binding. Phys. Chem. Chem. Phys., 8, 5166-5177.
-
(2006)
Phys. Chem. Chem. Phys.
, vol.8
, pp. 5166-5177
-
-
Huang, N.1
-
22
-
-
41449114598
-
Community benchmarks for virtual screening
-
Irwin, J. (2008) Community benchmarks for virtual screening. J. Comput.-Aided Mol. Des., 22, 193-199.
-
(2008)
J. Comput.-Aided Mol. Des.
, vol.22
, pp. 193-199
-
-
Irwin, J.1
-
23
-
-
0030255303
-
Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities
-
Jain, A.N. (1996) Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities. J. Comput.-Aided Mol. Des., 10, 427-440.
-
(1996)
J. Comput.-Aided Mol. Des.
, vol.10
, pp. 427-440
-
-
Jain, A.N.1
-
24
-
-
0028854034
-
Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
-
Jones, G. et al. (1995) Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J. Mol. Biol., 245, 43-53.
-
(1995)
J. Mol. Biol.
, vol.245
, pp. 43-53
-
-
Jones, G.1
-
25
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
Jones, G. et al. (1997) Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol., 267, 727-748.
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 727-748
-
-
Jones, G.1
-
26
-
-
8844263008
-
Docking and scoring in virtual screening for drug discovery: methods and applications
-
Kitchen, D.B. et al. (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat. Rev. Drug Discov., 3, 935-949.
-
(2004)
Nat. Rev. Drug Discov.
, vol.3
, pp. 935-949
-
-
Kitchen, D.B.1
-
27
-
-
20544447896
-
Knowledge based potentials: the reverse Boltzmann methodology, virtual screening and molecular weight dependence
-
Konstantinou Kirtay, C. et al. (2005) Knowledge based potentials: the reverse Boltzmann methodology, virtual screening and molecular weight dependence, QSAR Comb. Sci., 24, 527-536.
-
(2005)
QSAR Comb. Sci.
, vol.24
, pp. 527-536
-
-
KonstantinouKirtay, C.1
-
28
-
-
15244346501
-
LigScore: a novel scoring function for predicting binding affinities
-
Krammer, A. et al. (2005) LigScore: a novel scoring function for predicting binding affinities. J. Mol. Graph. Model., 23, 395-407.
-
(2005)
J. Mol. Graph. Model.
, vol.23
, pp. 395-407
-
-
Krammer, A.1
-
29
-
-
56449121765
-
Information theory-based scoring function for the structure-based prediction of protein-ligand binding affinity
-
Kulharia, M. et al. (2008) Information theory-based scoring function for the structure-based prediction of protein-ligand binding affinity. J. Chem. Inf. Model., 48, 1990-1998.
-
(2008)
J. Chem. Inf. Model.
, vol.48
, pp. 1990-1998
-
-
Kulharia, M.1
-
31
-
-
33749245117
-
Prediction of protein-ligand interactions. docking and scoring: successes and gaps
-
Leach, A.R. et al. (2006) Prediction of protein-ligand interactions. docking and scoring: successes and gaps. J. Med. Chem., 49, 5851-5855.
-
(2006)
J. Med. Chem.
, vol.49
, pp. 5851-5855
-
-
Leach, A.R.1
-
32
-
-
0000823044
-
BLEEP-potential of meanf orce describing protein-ligand interactions: I Generating potential
-
Mitchell, J.B.O. et al. (1999a) BLEEP-potential of meanf orce describing protein-ligand interactions: I. Generating potential. J. Comput. Chem., 20, 1165-1176.
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 1165-1176
-
-
Mitchell, J.B.O.1
-
33
-
-
0000882405
-
BLEEP-potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data
-
Mitchell, J.B.O. et al. (1999b) BLEEP-potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data. J. Comput. Chem., 20, 1177-1185.
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 1177-1185
-
-
Mitchell, J.B.O.1
-
34
-
-
40349087133
-
Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go
-
Moitessier, N. et al. (2008) Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. Br. J. Pharmacol., 153, S7-S26.
-
(2008)
Br. J. Pharmacol.
, vol.153
-
-
Moitessier, N.1
-
35
-
-
26444468103
-
General and targeted statistical potentials for protein-ligand interactions
-
Mooij, W.T.M. and Verdonk, M.L. (2005) General and targeted statistical potentials for protein-ligand interactions. Proteins: Struct., Funct., Bioinf., 61, 272-287.
-
(2005)
Proteins: Struct., Funct., Bioinf.
, vol.61
, pp. 272-287
-
-
Mooij, W.T.M.1
Verdonk, M.L.2
-
36
-
-
0033673508
-
A knowledge-based scoring function for protein-ligand interactions: probing the reference state
-
Muegge, I. (2000) A knowledge-based scoring function for protein-ligand interactions: probing the reference state. Perspect. Drug Discov. Des., 20, 99-114.
-
(2000)
Perspect. Drug Discov. Des.
, vol.20
, pp. 99-114
-
-
Muegge, I.1
-
37
-
-
0001745748
-
Effect of ligand volume correction on PMF scoring
-
Muegge, I. (2001) Effect of ligand volume correction on PMF scoring. J. Comput. Chem., 22, 418-425.
-
(2001)
J.Comput.Chem.
, vol.22
, pp. 418-425
-
-
Muegge, I.1
-
38
-
-
33749242403
-
PMF scoring revisited
-
Muegge, I. (2006) PMF scoring revisited. J. Med. Chem., 49, 5895-5902.
-
(2006)
J. Med. Chem.
, vol.49
, pp. 5895-5902
-
-
Muegge, I.1
-
39
-
-
0033545622
-
A general and fast scoring function for protein-ligand interactions: a simplified potential approach
-
Muegge, I. and Martin, Y.C. (1999) A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J. Med. Chem., 42, 791-804.
-
(1999)
J. Med. Chem.
, vol.42
, pp. 791-804
-
-
Muegge, I.1
Martin, Y.C.2
-
40
-
-
37349097759
-
y-Randomization and its variants in QSPR/QSAR
-
Rucker, C. et al. (2007) y-Randomization and its variants in QSPR/QSAR. J. Chem. Inf. Model., 47, 2345-2357.
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 2345-2357
-
-
Rucker, C.1
-
41
-
-
75749126524
-
Combining machine learning and pharmacophore-based interaction fingerprint for in silico screening
-
Sato, T. et al. (2010) Combining machine learning and pharmacophore-based interaction fingerprint for in silico screening. J. Chem. Inf. Model., 50, 170-185.
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 170-185
-
-
Sato, T.1
-
42
-
-
0345548657
-
Random forest: a classification and regression tool for compound classification and QSAR modeling
-
Svetnik, V. et al. (2003) Random forest: a classification and regression tool for compound classification and QSAR modeling. J. Chem. Inf. Comput. Sci., 43, 1947-1958.
-
(2003)
J. Chem. Inf. Comput. Sci.
, vol.43
, pp. 1947-1958
-
-
Svetnik, V.1
-
43
-
-
77952814305
-
-
The Discovery Studio Software, version 2.0. Accelrys Software Inc., San Diego, CA, USA
-
The Discovery Studio Software, version 2.0 (2001). Accelrys Software Inc., San Diego, CA, USA.
-
(2001)
-
-
-
44
-
-
77952859578
-
-
The Schrödinger Software, version 8.0. Schrödinger, LLC, New York, USA
-
The Schrödinger Software, version 8.0 (2005). Schrödinger, LLC, New York, USA.
-
(2005)
-
-
-
45
-
-
77952794049
-
-
The Sybyl Software, version 7.2. Tripos Inc., St Louis, MO, USA
-
The Sybyl Software, version 7.2 (2006). Tripos Inc., St Louis, MO, USA.
-
(2006)
-
-
-
46
-
-
26444588137
-
DrugScoreCSD - 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. et al. (2005) DrugScoreCSD - 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., 48, 6296-6303.
-
(2005)
J. Med. Chem.
, vol.48
, pp. 6296-6303
-
-
Velec, H.F.G.1
-
47
-
-
0036022960
-
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
-
Wang, R. et al. (2002) Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J. Comput.-Aided Mol. Des., 16, 11-26.
-
(2002)
J. Comput.-Aided Mol. Des.
, vol.16
, pp. 11-26
-
-
Wang, R.1
-
48
-
-
0037763817
-
Comparative evaluation of 11 scoring functions for molecular docking
-
Wang, R. et al. (2003) Comparative evaluation of 11 scoring functions for molecular docking. J. Med. Chem., 46, 2287-2303.
-
(2003)
J. Med. Chem.
, vol.46
, pp. 2287-2303
-
-
Wang, R.1
-
49
-
-
10044294023
-
An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes
-
Wang, R. et al. (2004) An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes. J. Chem. Inf. Comput. Sci., 44, 2114-2125.
-
(2004)
J. Chem. Inf. Comput. Sci.
, vol.44
, pp. 2114-2125
-
-
Wang, R.1
-
50
-
-
20444422149
-
The PDBbind database: methodologies and updates
-
Wang, R. et al. (2005) The PDBbind database: methodologies and updates. J. Med. Chem., 48, 4111-4119.
-
(2005)
J. Med. Chem.
, vol.48
, pp. 4111-4119
-
-
Wang, R.1
-
51
-
-
62849104063
-
Chemical probes that competitively and selectively inhibit Stat3 activation
-
Xu, X. et al. (2009) Chemical probes that competitively and selectively inhibit Stat3 activation. PLoS ONE, 4, e4783.
-
(2009)
PLoS ONE
, vol.4
-
-
Xu, X.1
|