-
1
-
-
64049102289
-
Binding of small-molecule ligands to proteins: "what you see" is not always "what you get"
-
Mobley DL, Dill KA, (2009) Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". Structure 17: 489-498.
-
(2009)
Structure
, vol.17
, pp. 489-498
-
-
Mobley, D.L.1
Dill, K.A.2
-
2
-
-
77954274507
-
Evaluation of the performance of four molecular docking programs on a diverse set of protein-ligand complexes
-
Li X, Li Y, Cheng T, Liu Z, Wang R, (2010) Evaluation of the performance of four molecular docking programs on a diverse set of protein-ligand complexes. J Comput Chem 31: 2109-2125.
-
(2010)
J Comput Chem
, vol.31
, pp. 2109-2125
-
-
Li, X.1
Li, Y.2
Cheng, T.3
Liu, Z.4
Wang, R.5
-
3
-
-
76149120388
-
AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
-
Trott O, Olson AJ, (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31: 455-461.
-
(2010)
J Comput Chem
, vol.31
, pp. 455-461
-
-
Trott, O.1
Olson, A.J.2
-
4
-
-
77957820654
-
Virtual screening for HIV protease inhibitors: a comparison of AutoDock 4 and Vina
-
Chang MW, Ayeni C, Breuer S, Torbett BE, (2010) Virtual screening for HIV protease inhibitors: a comparison of AutoDock 4 and Vina. PLoS One 5: e11955.
-
(2010)
PLoS One
, vol.5
-
-
Chang, M.W.1
Ayeni, C.2
Breuer, S.3
Torbett, B.E.4
-
5
-
-
77950908360
-
A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction
-
Cheng T, Liu Z, Wang R, (2010) A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction. BMC Bioinformatics 11: 193.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 193
-
-
Cheng, T.1
Liu, Z.2
Wang, R.3
-
6
-
-
0036022960
-
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
-
Wang R, Lai L, Wang S, (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
Lai, L.2
Wang, S.3
-
8
-
-
72449154625
-
Thermodynamic analysis of mRNA cap binding by the human initiation factor eIF4E via free energy perturbations
-
Guimaraes CR, Kopecky DJ, Mihalic J, Shen S, Jeffries S, et al. (2009) Thermodynamic analysis of mRNA cap binding by the human initiation factor eIF4E via free energy perturbations. J Am Chem Soc 131: 18139-18146.
-
(2009)
J Am Chem Soc
, vol.131
, pp. 18139-18146
-
-
Guimaraes, C.R.1
Kopecky, D.J.2
Mihalic, J.3
Shen, S.4
Jeffries, S.5
-
9
-
-
65449150253
-
An effective docking strategy for virtual screening based on multi-objective optimization algorithm
-
Li H, Zhang H, Zheng M, Luo J, Kang L, et al. (2009) An effective docking strategy for virtual screening based on multi-objective optimization algorithm. BMC Bioinformatics 10: 58.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 58
-
-
Li, H.1
Zhang, H.2
Zheng, M.3
Luo, J.4
Kang, L.5
-
10
-
-
45749133178
-
Bootstrap-based consensus scoring method for protein-ligand docking
-
Fukunishi H, Teramoto R, Takada T, Shimada J, (2008) Bootstrap-based consensus scoring method for protein-ligand docking. J Chem Inf Model 48: 988-996.
-
(2008)
J Chem Inf Model
, vol.48
, pp. 988-996
-
-
Fukunishi, H.1
Teramoto, R.2
Takada, T.3
Shimada, J.4
-
11
-
-
77958585233
-
NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexes
-
Durrant JD, McCammon JA, (2010) NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexes. J Chem Inf Model 50: 1865-1871.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 1865-1871
-
-
Durrant, J.D.1
McCammon, J.A.2
-
12
-
-
77949318457
-
Predicting protein complex geometries with a neural network
-
10.1002/prot.22626
-
Chae MH, Krull F, Lorenzen S, Knapp EW, (2010) Predicting protein complex geometries with a neural network. Proteins 78: 1026-1039 10.1002/prot.22626.
-
(2010)
Proteins
, vol.78
, pp. 1026-1039
-
-
Chae, M.H.1
Krull, F.2
Lorenzen, S.3
Knapp, E.W.4
-
13
-
-
0022471098
-
Learning representations by back-propagating error
-
Rumelhart DE, Hinton GE, Williams RJ, (1986) Learning representations by back-propagating error. Nature 323: 533-536.
-
(1986)
Nature
, vol.323
, pp. 533-536
-
-
Rumelhart, D.E.1
Hinton, G.E.2
Williams, R.J.3
-
14
-
-
0034645763
-
Knowledge-based scoring function to predict protein-ligand interactions
-
Gohlke H, Hendlich M, Klebe G, (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
Hendlich, M.2
Klebe, G.3
-
15
-
-
77958567426
-
Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening
-
Brylinski M, Skolnick J, (2010) Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening. J Chem Inf Model 50: 1839-1854.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 1839-1854
-
-
Brylinski, M.1
Skolnick, J.2
-
16
-
-
70349211752
-
Automated docking screens: a feasibility study
-
Irwin JJ, Shoichet BK, Mysinger MM, Huang N, Colizzi F, et al. (2009) Automated docking screens: a feasibility study. J Med Chem 52: 5712-5720.
-
(2009)
J Med Chem
, vol.52
, pp. 5712-5720
-
-
Irwin, J.J.1
Shoichet, B.K.2
Mysinger, M.M.3
Huang, N.4
Colizzi, F.5
-
17
-
-
77649204282
-
Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists
-
Katritch V, Jaakola VP, Lane JR, Lin J, Ijzerman AP, et al. (2010) Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists. J Med Chem 53: 1799-1809.
-
(2010)
J Med Chem
, vol.53
, pp. 1799-1809
-
-
Katritch, V.1
Jaakola, V.P.2
Lane, J.R.3
Lin, J.4
Ijzerman, A.P.5
-
18
-
-
77957841701
-
Pharmacophore modeling and virtual screening studies for new VEGFR-2 kinase inhibitors
-
Lee K, Jeong KW, Lee Y, Song JY, Kim MS, et al. (2010) Pharmacophore modeling and virtual screening studies for new VEGFR-2 kinase inhibitors. Eur J Med Chem 45: 5420-5427.
-
(2010)
Eur J Med Chem
, vol.45
, pp. 5420-5427
-
-
Lee, K.1
Jeong, K.W.2
Lee, Y.3
Song, J.Y.4
Kim, M.S.5
-
19
-
-
78651521685
-
The discovery of potential acetylcholinesterase inhibitors: a combination of pharmacophore modeling, virtual screening, and molecular docking studies
-
Lu SH, Wu JW, Liu HL, Zhao JH, Liu KT, et al. (2011) The discovery of potential acetylcholinesterase inhibitors: a combination of pharmacophore modeling, virtual screening, and molecular docking studies. J Biomed Sci 18: 8.
-
(2011)
J Biomed Sci
, vol.18
, pp. 8
-
-
Lu, S.H.1
Wu, J.W.2
Liu, H.L.3
Zhao, J.H.4
Liu, K.T.5
-
20
-
-
66149142757
-
Consensus scoring for enriching near-native structures from protein-protein docking decoys
-
Liang S, Meroueh SO, Wang G, Qiu C, Zhou Y, (2009) Consensus scoring for enriching near-native structures from protein-protein docking decoys. Proteins 75: 397-403.
-
(2009)
Proteins
, vol.75
, pp. 397-403
-
-
Liang, S.1
Meroueh, S.O.2
Wang, G.3
Qiu, C.4
Zhou, Y.5
-
21
-
-
77957225016
-
Test MM-PB/SA on true conformational ensembles of protein-ligand complexes
-
Li Y, Liu Z, Wang R, (2010) Test MM-PB/SA on true conformational ensembles of protein-ligand complexes. J Chem Inf Model 50: 1682-1692.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 1682-1692
-
-
Li, Y.1
Liu, Z.2
Wang, R.3
-
22
-
-
0001160588
-
What size net gives valid generalization?
-
Baum EB, Haussler D, (1989) What size net gives valid generalization? Neural Computation 1: 151-160.
-
(1989)
Neural Computation
, vol.1
, pp. 151-160
-
-
Baum, E.B.1
Haussler, D.2
-
23
-
-
2542530042
-
The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures
-
Wang R, Fang X, Lu Y, Wang S, (2004) The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J Med Chem 47: 2977-2980.
-
(2004)
J Med Chem
, vol.47
, pp. 2977-2980
-
-
Wang, R.1
Fang, X.2
Lu, Y.3
Wang, S.4
-
24
-
-
33750991346
-
Benchmarking sets for molecular docking
-
Huang N, Shoichet BK, Irwin JJ, (2006) Benchmarking sets for molecular docking. J Med Chem 49: 6789-6801.
-
(2006)
J Med Chem
, vol.49
, pp. 6789-6801
-
-
Huang, N.1
Shoichet, B.K.2
Irwin, J.J.3
-
25
-
-
41449114598
-
Community benchmarks for virtual screening
-
Irwin JJ, (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.J.1
-
26
-
-
77957281518
-
Relating the shape of protein binding sites to binding affinity profiles: is there an association?
-
Simon Z, Vigh-Smeller M, Peragovics A, Csukly G, Zahoranszky-Kohalmi G, et al. (2010) Relating the shape of protein binding sites to binding affinity profiles: is there an association? BMC Struct Biol 10: 32.
-
(2010)
BMC Struct Biol
, vol.10
, pp. 32
-
-
Simon, Z.1
Vigh-Smeller, M.2
Peragovics, A.3
Csukly, G.4
Zahoranszky-Kohalmi, G.5
-
27
-
-
80255127565
-
Ligand supported homology modeling and docking evaluation of CCR2: docked pose selection by consensus scoring
-
Kim JH, Lim JW, Lee SW, Kim K, No KT, (2011) Ligand supported homology modeling and docking evaluation of CCR2: docked pose selection by consensus scoring. J Mol Model.
-
(2011)
J Mol Model
-
-
Kim, J.H.1
Lim, J.W.2
Lee, S.W.3
Kim, K.4
No, K.T.5
-
28
-
-
77958562342
-
Computational analysis of HIV-1 protease protein binding pockets
-
Ko GM, Reddy AS, Kumar S, Bailey BA, Garg R, (2010) Computational analysis of HIV-1 protease protein binding pockets. J Chem Inf Model 50: 1759-1771.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 1759-1771
-
-
Ko, G.M.1
Reddy, A.S.2
Kumar, S.3
Bailey, B.A.4
Garg, R.5
-
29
-
-
49649114605
-
Protein structure modeling with MODELLER
-
Eswar N, Eramian D, Webb B, Shen MY, Sali A, (2008) Protein structure modeling with MODELLER. Methods Mol Biol 426: 145-159.
-
(2008)
Methods Mol Biol
, vol.426
, pp. 145-159
-
-
Eswar, N.1
Eramian, D.2
Webb, B.3
Shen, M.Y.4
Sali, A.5
-
30
-
-
77956019866
-
FLAP: GRID molecular interaction fields in virtual screening. validation using the DUD data set
-
Cross S, Baroni M, Carosati E, Benedetti P, Clementi S, (2010) FLAP: GRID molecular interaction fields in virtual screening. validation using the DUD data set. J Chem Inf Model 50: 1442-1450.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 1442-1450
-
-
Cross, S.1
Baroni, M.2
Carosati, E.3
Benedetti, P.4
Clementi, S.5
-
31
-
-
77955560416
-
QSAR studies of bioactivities of 1-(azacyclyl)-3-arylsulfonyl-1H-pyrrolo[2,3-b]pyridines as 5-HT6 receptor ligands using physicochemical descriptors and MLR and ANN-modeling
-
Goodarzi M, Freitas MP, Ghasemi N, (2010) QSAR studies of bioactivities of 1-(azacyclyl)-3-arylsulfonyl-1H-pyrrolo[2,3-b]pyridines as 5-HT6 receptor ligands using physicochemical descriptors and MLR and ANN-modeling. Eur J Med Chem 45: 3911-3915.
-
(2010)
Eur J Med Chem
, vol.45
, pp. 3911-3915
-
-
Goodarzi, M.1
Freitas, M.P.2
Ghasemi, N.3
-
32
-
-
65249142225
-
Comparison of ligand- and structure-based virtual screening on the DUD data set
-
von KM, Freyss J, Sander T, (2009) Comparison of ligand- and structure-based virtual screening on the DUD data set. J Chem Inf Model 49: 209-231.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 209-231
-
-
von, K.M.1
Freyss, J.2
Sander, T.3
-
33
-
-
33947420139
-
Shape variation in protein binding pockets and their ligands
-
Kahraman A, Morris RJ, Laskowski RA, Thornton JM, (2007) Shape variation in protein binding pockets and their ligands. J Mol Biol 368: 283-301.
-
(2007)
J Mol Biol
, vol.368
, pp. 283-301
-
-
Kahraman, A.1
Morris, R.J.2
Laskowski, R.A.3
Thornton, J.M.4
-
34
-
-
68949158347
-
A statistical framework to evaluate virtual screening
-
Zhao W, Hevener KE, White SW, Lee RE, Boyett JM, (2009) A statistical framework to evaluate virtual screening. BMC Bioinformatics 10: 225.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 225
-
-
Zhao, W.1
Hevener, K.E.2
White, S.W.3
Lee, R.E.4
Boyett, J.M.5
-
35
-
-
0033397980
-
Python: a programming language for software integration and development
-
Sanner MF, (1999) Python: a programming language for software integration and development. J Mol Graph Model 17: 57-61.
-
(1999)
J Mol Graph Model
, vol.17
, pp. 57-61
-
-
Sanner, M.F.1
-
36
-
-
44649101872
-
The effect of different electrostatic potentials on docking accuracy: a case study using DOCK5.4
-
Tsai KC, Wang SH, Hsiao NW, Li M, Wang B, (2008) The effect of different electrostatic potentials on docking accuracy: a case study using DOCK5.4. Bioorg Med Chem Lett 18: 3509-3512.
-
(2008)
Bioorg Med Chem Lett
, vol.18
, pp. 3509-3512
-
-
Tsai, K.C.1
Wang, S.H.2
Hsiao, N.W.3
Li, M.4
Wang, B.5
-
37
-
-
77958565592
-
Binding energy landscape analysis helps to discriminate true hits from high-scoring decoys in virtual screening
-
Wei D, Zheng H, Su N, Deng M, Lai L, (2010) Binding energy landscape analysis helps to discriminate true hits from high-scoring decoys in virtual screening. J Chem Inf Model 50: 1855-1864.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 1855-1864
-
-
Wei, D.1
Zheng, H.2
Su, N.3
Deng, M.4
Lai, L.5
|