-
1
-
-
77950503976
-
Virtual screening: an endless staircase?
-
Schneider G. Virtual screening: an endless staircase? Nat Rev Drug Discov 2010, 9:273-276.
-
(2010)
Nat Rev Drug Discov
, vol.9
, pp. 273-276
-
-
Schneider, G.1
-
2
-
-
70249148040
-
Mining free compound databases to identify candidates selected by virtual screening
-
Vasudevan SR, Churchill GC. Mining free compound databases to identify candidates selected by virtual screening. Expert Opin Drug Discov 2009, 4:901-906.
-
(2009)
Expert Opin Drug Discov
, vol.4
, pp. 901-906
-
-
Vasudevan, S.R.1
Churchill, G.C.2
-
3
-
-
34548289911
-
Free resources to assist structure-based virtual ligand screening experiments
-
Villoutreix BO, Renault N, Lagorce D, Sperandio O, Montes M, Miteva MA. Free resources to assist structure-based virtual ligand screening experiments. Curr Protein Pept Sci 2007, 8:381-411.
-
(2007)
Curr Protein Pept Sci
, vol.8
, pp. 381-411
-
-
Villoutreix, B.O.1
Renault, N.2
Lagorce, D.3
Sperandio, O.4
Montes, M.5
Miteva, M.A.6
-
4
-
-
79952254027
-
Discovery of potent inhibitors of soluble epoxide hydrolase by combinatorial library design and structure-based virtual screening
-
Xing L, McDonald JJ, Kolodziej SA, Kurumbail RG, Williams JM, Warren CJ, O'Neal JM, Skepner JE, Roberds SL. Discovery of potent inhibitors of soluble epoxide hydrolase by combinatorial library design and structure-based virtual screening. J Med Chem 2011, 54:1211-1222.
-
(2011)
J Med Chem
, vol.54
, pp. 1211-1222
-
-
Xing, L.1
McDonald, J.J.2
Kolodziej, S.A.3
Kurumbail, R.G.4
Williams, J.M.5
Warren, C.J.6
O'Neal, J.M.7
Skepner, J.E.8
Roberds, S.L.9
-
5
-
-
34547939672
-
Structure-based activity prediction for an enzyme of unknown function
-
Hermann JC, Marti-Arbona R, Fedorov AA, Fedorov E, Almo SC, Shoichet BK, Raushel FM. Structure-based activity prediction for an enzyme of unknown function. Nature 2007, 448:775-779.
-
(2007)
Nature
, vol.448
, pp. 775-779
-
-
Hermann, J.C.1
Marti-Arbona, R.2
Fedorov, A.A.3
Fedorov, E.4
Almo, S.C.5
Shoichet, B.K.6
Raushel, F.M.7
-
6
-
-
36849044810
-
-
TR 06-028, Department of Computer Science and Engineering, University of Minnesota, Twin Cities
-
Pandey G, Kumar V, Steinbach M: Computational Approaches for Protein Function Prediction: A Survey. TR 06-028, Department of Computer Science and Engineering, University of Minnesota, Twin Cities, 2006.
-
(2006)
Computational Approaches for Protein Function Prediction: A Survey
-
-
Pandey, G.1
Kumar, V.2
Steinbach, M.3
-
7
-
-
67649225348
-
Efficient drug lead discovery and optimization
-
Jorgensen WL. Efficient drug lead discovery and optimization. Acc Chem Res 2009, 42:724-733.
-
(2009)
Acc Chem Res
, vol.42
, pp. 724-733
-
-
Jorgensen, W.L.1
-
8
-
-
34249038325
-
Lead optimization via high-throughput molecular docking
-
Joseph-McCarthy D, Baber JC, Feyfant E, Thompson DC, Humblet C. Lead optimization via high-throughput molecular docking. Curr Opin Drug Discov Devel 2007, 10:264-274.
-
(2007)
Curr Opin Drug Discov Devel
, vol.10
, pp. 264-274
-
-
Joseph-McCarthy, D.1
Baber, J.C.2
Feyfant, E.3
Thompson, D.C.4
Humblet, C.5
-
9
-
-
33749245117
-
Prediction of protein-ligand interactions. Docking and scoring: successes and gaps
-
Leach AR, Shoichet BK, Peishoff CE. 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
-
10
-
-
84861118556
-
Outstanding challenges in protein-ligand docking and structure-based virtual screening
-
Waszkowycz B, Clark DE, Gancia E. Outstanding challenges in protein-ligand docking and structure-based virtual screening. WIREs Comput Mol Sci 2011, 1:229-259.
-
(2011)
WIREs Comput Mol Sci
, vol.1
, pp. 229-259
-
-
Waszkowycz, B.1
Clark, D.E.2
Gancia, E.3
-
11
-
-
33750898990
-
Molecular mechanics methods for predicting protein-ligand binding
-
Huang N, Kalyanaraman C, Bernacki K, Jacobson MP. Molecular mechanics methods for predicting protein-ligand binding. Phys Chem Chem Phys 2006, 8:5166-5177.
-
(2006)
Phys Chem Chem Phys
, vol.8
, pp. 5166-5177
-
-
Huang, N.1
Kalyanaraman, C.2
Bernacki, K.3
Jacobson, M.P.4
-
12
-
-
26444468103
-
General and targeted statistical potentials for protein-ligand interactions
-
Mooij WTM, Verdonk ML. General and targeted statistical potentials for protein-ligand interactions. Proteins 2005, 61:272-287.
-
(2005)
Proteins
, vol.61
, pp. 272-287
-
-
Mooij, W.T.M.1
Verdonk, M.L.2
-
13
-
-
0034645763
-
Knowledge-based scoring function to predict protein-ligand interactions
-
Gohlke H, Hendlich M, Klebe G. Knowledge-based scoring function to predict protein-ligand interactions. J Mol Biol 2000, 295:337-356.
-
(2000)
J Mol Biol
, vol.295
, pp. 337-356
-
-
Gohlke, H.1
Hendlich, M.2
Klebe, G.3
-
14
-
-
12144289984
-
Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
-
Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, et al. 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
-
15
-
-
15244346501
-
LigScore: a novel scoring function for predicting binding affinities
-
Krammer A, Kirchhoff PD, Jiang X, Venkatachalam CM, Waldman M. LigScore: a novel scoring function for predicting binding affinities. J Mol Graph Model 2005, 23:395-407.
-
(2005)
J Mol Graph Model
, vol.23
, pp. 395-407
-
-
Krammer, A.1
Kirchhoff, P.D.2
Jiang, X.3
Venkatachalam, C.M.4
Waldman, M.5
-
16
-
-
84857453882
-
Let's get honest about sampling
-
Mobley DL. Let's get honest about sampling. J Comput Mol Des 2012, 26:93-95.
-
(2012)
J Comput Mol Des
, vol.26
, pp. 93-95
-
-
Mobley, D.L.1
-
17
-
-
60349109713
-
Computational evaluation of protein-small molecule binding
-
Guvench O, MacKerell AD. Computational evaluation of protein-small molecule binding. Curr Opin Struct Biol 2009, 19:56-61.
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 56-61
-
-
Guvench, O.1
MacKerell, A.D.2
-
18
-
-
77952825581
-
A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking
-
Ballester PJ, Mitchell JBO. A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking. Bioinformatics 2010, 26:1169-1175.
-
(2010)
Bioinformatics
, vol.26
, pp. 1169-1175
-
-
Ballester, P.J.1
Mitchell, J.B.O.2
-
19
-
-
77950022453
-
Non-additivity of functional group contributions in protein-ligand binding: a comprehensive study by crystallography and isothermal titration calorimetry
-
Baum B, Muley L, Smolinski M, Heine A, Hangauer D, Klebe G. Non-additivity of functional group contributions in protein-ligand binding: a comprehensive study by crystallography and isothermal titration calorimetry. J Mol Biol 2010, 397:1042-1054.
-
(2010)
J Mol Biol
, vol.397
, pp. 1042-1054
-
-
Baum, B.1
Muley, L.2
Smolinski, M.3
Heine, A.4
Hangauer, D.5
Klebe, G.6
-
20
-
-
84923588607
-
Improving AutoDock Vina using random forest: the growing accuracy of binding affinity prediction by the effective exploitation of larger data sets
-
Li H, Leung K-S, Wong M-H, Ballester PJ. Improving AutoDock Vina using random forest: the growing accuracy of binding affinity prediction by the effective exploitation of larger data sets. Mol Inform 2015, 34:115-126.
-
(2015)
Mol Inform
, vol.34
, pp. 115-126
-
-
Li, H.1
Leung, K.-S.2
Wong, M.-H.3
Ballester, P.J.4
-
21
-
-
77957898063
-
Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions
-
Huang S-Y, Grinter SZ, Zou X. Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions. Phys Chem Chem Phys 2010, 12:12899-12908.
-
(2010)
Phys Chem Chem Phys
, vol.12
, pp. 12899-12908
-
-
Huang, S.-Y.1
Grinter, S.Z.2
Zou, X.3
-
22
-
-
84862795414
-
Structure-based virtual screening for drug discovery: a problem-centric review
-
Cheng T, Li Q, Zhou Z, Wang Y, Bryant SH. Structure-based virtual screening for drug discovery: a problem-centric review. AAPS J 2012, 14:133-141.
-
(2012)
AAPS J
, vol.14
, pp. 133-141
-
-
Cheng, T.1
Li, Q.2
Zhou, Z.3
Wang, Y.4
Bryant, S.H.5
-
23
-
-
84871717368
-
Scoring functions for protein-ligand interactions
-
In: 1st ed. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA.
-
Sotriffer C. Scoring functions for protein-ligand interactions. In: Protein-Ligand Interactions. 1st ed. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA; 2012.
-
(2012)
Protein-Ligand Interactions
-
-
Sotriffer, C.1
-
24
-
-
84863598108
-
Bioinformatics and variability in drug response: a protein structural perspective
-
Lahti JL, Tang GW, Capriotti E, Liu T, Altman RB. Bioinformatics and variability in drug response: a protein structural perspective. J R Soc Interface 2012, 9:1409-1437.
-
(2012)
J R Soc Interface
, vol.9
, pp. 1409-1437
-
-
Lahti, J.L.1
Tang, G.W.2
Capriotti, E.3
Liu, T.4
Altman, R.B.5
-
25
-
-
84873686290
-
Drug repositioning by structure-based virtual screening
-
Ma D-L, Chan DS-H, Leung C-H. Drug repositioning by structure-based virtual screening. Chem Soc Rev 2013, 42:2130-2141.
-
(2013)
Chem Soc Rev
, vol.42
, pp. 2130-2141
-
-
Ma, D.-L.1
Chan, D.-H.2
Leung, C.-H.3
-
26
-
-
84941075640
-
Improvements, trends, and new ideas in molecular docking: 2012-2013 in review
-
Yuriev E, Holien J, Ramsland PA. Improvements, trends, and new ideas in molecular docking: 2012-2013 in review. J Mol Recognit 2015.
-
(2015)
J Mol Recognit
-
-
Yuriev, E.1
Holien, J.2
Ramsland, P.A.3
-
27
-
-
65749110436
-
Computational intelligence methods for docking scores
-
Hecht D, Fogel GB. Computational intelligence methods for docking scores. Curr Comput - Aided Drug Des 2009, 5:56-68.
-
(2009)
Curr Comput - Aided Drug Des
, vol.5
, pp. 56-68
-
-
Hecht, D.1
Fogel, G.B.2
-
28
-
-
84884672908
-
Experimental versus predicted affinities for ligand binding to estrogen receptor: iterative selection and rescoring of docked poses systematically improves the correlation
-
Wright JS, Anderson JM, Shadnia H, Durst T, Katzenellenbogen JA. Experimental versus predicted affinities for ligand binding to estrogen receptor: iterative selection and rescoring of docked poses systematically improves the correlation. J Comput Aided Mol Des 2013.
-
(2013)
J Comput Aided Mol Des
-
-
Wright, J.S.1
Anderson, J.M.2
Shadnia, H.3
Durst, T.4
Katzenellenbogen, J.A.5
-
29
-
-
33746867935
-
GFscore: a general nonlinear consensus scoring function for high-throughput docking
-
Betzi S, Suhre K, Chétrit B, Guerlesquin F, Morelli X. GFscore: a general nonlinear consensus scoring function for high-throughput docking. J Chem Inf Model 2006, 46:1704-1712.
-
(2006)
J Chem Inf Model
, vol.46
, pp. 1704-1712
-
-
Betzi, S.1
Suhre, K.2
Chétrit, B.3
Guerlesquin, F.4
Morelli, X.5
-
30
-
-
84874445951
-
Consensus docking: improving the reliability of docking in a virtual screening context
-
Houston DR, Walkinshaw MD. Consensus docking: improving the reliability of docking in a virtual screening context. J Chem Inf Model 2013, 53:384-390.
-
(2013)
J Chem Inf Model
, vol.53
, pp. 384-390
-
-
Houston, D.R.1
Walkinshaw, M.D.2
-
31
-
-
84862848391
-
Machine learning methods for property prediction in chemoinformatics: quo vadis?
-
Varnek A, Baskin I. Machine learning methods for property prediction in chemoinformatics: quo vadis? J Chem Inf Model 2012, 52:1413-1437.
-
(2012)
J Chem Inf Model
, vol.52
, pp. 1413-1437
-
-
Varnek, A.1
Baskin, I.2
-
33
-
-
84866686849
-
Machine learning techniques and drug design
-
Gertrudes JC, Maltarollo VG, Silva RA, Oliveira PR, Honório KM, da Silva ABF. Machine learning techniques and drug design. Curr Med Chem 2012, 19:4289-4297.
-
(2012)
Curr Med Chem
, vol.19
, pp. 4289-4297
-
-
Gertrudes, J.C.1
Maltarollo, V.G.2
Silva, R.A.3
Oliveira, P.R.4
Honório, K.M.5
da Silva, A.B.F.6
-
34
-
-
35748932917
-
A review of feature selection techniques in bioinformatics
-
Saeys Y, Inza I, Larrañaga P. A review of feature selection techniques in bioinformatics. Bioinformatics 2007, 23:2507-2517.
-
(2007)
Bioinformatics
, vol.23
, pp. 2507-2517
-
-
Saeys, Y.1
Inza, I.2
Larrañaga, P.3
-
35
-
-
84864837998
-
Predictive cheminformatics in drug discovery: statistical modeling for analysis of micro-array and gene expression data
-
In: Larson RS, Walker JM, eds. New York: Humana Press;
-
Sukumar N, Krein MP, Embrechts MJ. Predictive cheminformatics in drug discovery: statistical modeling for analysis of micro-array and gene expression data. In: Larson RS, Walker JM, eds. Bioinformatics and Drug Discovery, vol. 910. New York: Humana Press; 2012, 165-194.
-
(2012)
Bioinformatics and Drug Discovery
, vol.910
, pp. 165-194
-
-
Sukumar, N.1
Krein, M.P.2
Embrechts, M.J.3
-
36
-
-
66149103553
-
Comparative assessment of scoring functions on a diverse test set
-
Cheng T, Li X, Li Y, Liu Z, Wang R. Comparative assessment of scoring functions on a diverse test set. J Chem Inf Model 2009, 49:1079-1093.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 1079-1093
-
-
Cheng, T.1
Li, X.2
Li, Y.3
Liu, Z.4
Wang, R.5
-
37
-
-
84903287174
-
Comparative assessment of scoring functions on an updated benchmark: 2. Evaluation methods and general results
-
Li Y, Han L, Liu Z, Wang R. Comparative assessment of scoring functions on an updated benchmark: 2. Evaluation methods and general results. J Chem Inf Model 2014, 54:1717-1736.
-
(2014)
J Chem Inf Model
, vol.54
, pp. 1717-1736
-
-
Li, Y.1
Han, L.2
Liu, Z.3
Wang, R.4
-
38
-
-
80053330055
-
CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions
-
Smith RD, Dunbar JB, Ung PM-U, Esposito EX, Yang C-Y, Wang S, Carlson HA. CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions. J Chem Inf Model 2011, 51:2115-2131.
-
(2011)
J Chem Inf Model
, vol.51
, pp. 2115-2131
-
-
Smith, R.D.1
Dunbar, J.B.2
Ung, P.-U.3
Esposito, E.X.4
Yang, C.-Y.5
Wang, S.6
Carlson, H.A.7
-
39
-
-
34247272948
-
Evaluating virtual screening methods: good and bad metrics for the 'early recognition' problem
-
Truchon J-F, Bayly CI. Evaluating virtual screening methods: good and bad metrics for the 'early recognition' problem. J Chem Inf Model 2007, 47:488-508.
-
(2007)
J Chem Inf Model
, vol.47
, pp. 488-508
-
-
Truchon, J.-F.1
Bayly, C.I.2
-
40
-
-
17144385534
-
Virtual screening workflow development guided by the 'receiver operating characteristic' curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4
-
Triballeau N, Acher F, Brabet I, Pin J-P, Bertrand H-O. Virtual screening workflow development guided by the 'receiver operating characteristic' curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4. J Med Chem 2005, 48:2534-2547.
-
(2005)
J Med Chem
, vol.48
, pp. 2534-2547
-
-
Triballeau, N.1
Acher, F.2
Brabet, I.3
Pin, J.-P.4
Bertrand, H.-O.5
-
41
-
-
78650643212
-
Ultrafast shape recognition: method and applications
-
Ballester PJ. Ultrafast shape recognition: method and applications. Future Med Chem 2011, 3:65-78.
-
(2011)
Future Med Chem
, vol.3
, pp. 65-78
-
-
Ballester, P.J.1
-
42
-
-
77952832818
-
A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval
-
Swamidass SJ, Azencott C-A, Daily K, Baldi P. A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval. Bioinformatics 2010, 26:1348-1356.
-
(2010)
Bioinformatics
, vol.26
, pp. 1348-1356
-
-
Swamidass, S.J.1
Azencott, C.-A.2
Daily, K.3
Baldi, P.4
-
43
-
-
68949158347
-
A statistical framework to evaluate virtual screening
-
Zhao W, Hevener KE, White SW, Lee RE, Boyett JM. A statistical framework to evaluate virtual screening. BMC Bioinformatics 2009, 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
-
44
-
-
33750991346
-
Benchmarking sets for molecular docking
-
Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem 2006, 49:6789-6801.
-
(2006)
J Med Chem
, vol.49
, pp. 6789-6801
-
-
Huang, N.1
Shoichet, B.K.2
Irwin, J.J.3
-
45
-
-
65349136650
-
Maximum unbiased validation (MUV) data sets for virtual screening based on PubChem bioactivity data
-
Rohrer SG, Baumann K. Maximum unbiased validation (MUV) data sets for virtual screening based on PubChem bioactivity data. J Chem Inf Model 2009, 49:169-184.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 169-184
-
-
Rohrer, S.G.1
Baumann, K.2
-
46
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
Warren GL, Andrews CW, Capelli A-M, Clarke B, LaLonde J, Lambert MH, Lindvall M, Nevins N, Semus SF, Senger S, et al. 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
-
47
-
-
1842740026
-
Predicting protein-ligand binding affinities using novel geometrical descriptors and machine-learning methods
-
Deng W, Breneman C, Embrechts MJ. Predicting protein-ligand binding affinities using novel geometrical descriptors and machine-learning methods. J Chem Inf Comput Sci 2004, 44:699-703.
-
(2004)
J Chem Inf Comput Sci
, vol.44
, pp. 699-703
-
-
Deng, W.1
Breneman, C.2
Embrechts, M.J.3
-
48
-
-
84984286248
-
A PLS kernel algorithm for data sets with many variables and fewer objects. Part 1: theory and algorithm
-
Rännar S, Lindgren F, Geladi P, Wold S. A PLS kernel algorithm for data sets with many variables and fewer objects. Part 1: theory and algorithm. J Chemom 1994, 8:111-125.
-
(1994)
J Chemom
, vol.8
, pp. 111-125
-
-
Rännar, S.1
Lindgren, F.2
Geladi, P.3
Wold, S.4
-
49
-
-
33646462126
-
Development of quantitative structure-binding affinity relationship models based on novel geometrical chemical descriptors of the protein-ligand interfaces
-
Zhang S, Golbraikh A, Tropsha A. Development of quantitative structure-binding affinity relationship models based on novel geometrical chemical descriptors of the protein-ligand interfaces. J Med Chem 2006, 49:2713-2724.
-
(2006)
J Med Chem
, vol.49
, pp. 2713-2724
-
-
Zhang, S.1
Golbraikh, A.2
Tropsha, A.3
-
50
-
-
42149142447
-
Distance dependent scoring function for describing protein-ligand intermolecular interactions
-
Artemenko N. Distance dependent scoring function for describing protein-ligand intermolecular interactions. J Chem Inf Model 2008, 48:569-574.
-
(2008)
J Chem Inf Model
, vol.48
, pp. 569-574
-
-
Artemenko, N.1
-
51
-
-
77649229098
-
Binding affinity prediction with property-encoded shape distribution signatures
-
Das S, Krein MP, Breneman CM. Binding affinity prediction with property-encoded shape distribution signatures. J Chem Inf Model 2010, 50:298-308.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 298-308
-
-
Das, S.1
Krein, M.P.2
Breneman, C.M.3
-
52
-
-
52249113723
-
SFCscore: scoring functions for affinity prediction of protein-ligand complexes
-
Sotriffer CA, Sanschagrin P, Matter H, Klebe G. SFCscore: scoring functions for affinity prediction of protein-ligand complexes. Proteins 2008, 73:395-419.
-
(2008)
Proteins
, vol.73
, pp. 395-419
-
-
Sotriffer, C.A.1
Sanschagrin, P.2
Matter, H.3
Klebe, G.4
-
53
-
-
77958585233
-
NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexes
-
Durrant JD, McCammon JA. NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexes. J Chem Inf Model 2010, 50:1865-1871.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 1865-1871
-
-
Durrant, J.D.1
McCammon, J.A.2
-
54
-
-
76149120388
-
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
-
Trott O, Olson AJ. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 2010, 31:455-461.
-
(2010)
J Comput Chem
, vol.31
, pp. 455-461
-
-
Trott, O.1
Olson, A.J.2
-
55
-
-
79953277006
-
BINANA: a novel algorithm for ligand-binding characterization
-
Durrant JD, McCammon JA. BINANA: a novel algorithm for ligand-binding characterization. J Mol Graph Model 2011, 29:888-893.
-
(2011)
J Mol Graph Model
, vol.29
, pp. 888-893
-
-
Durrant, J.D.1
McCammon, J.A.2
-
56
-
-
82355181271
-
Cscore: a simple yet effective scoring function for protein-ligand binding affinity prediction using modified Cmac learning architecture
-
Ouyang X, Handoko SD, Kwoh CK. Cscore: a simple yet effective scoring function for protein-ligand binding affinity prediction using modified Cmac learning architecture. J Bioinform Comput Biol 2011, 09:1-14.
-
(2011)
J Bioinform Comput Biol
, vol.9
, pp. 1-14
-
-
Ouyang, X.1
Handoko, S.D.2
Kwoh, C.K.3
-
57
-
-
84896705093
-
Combining machine learning systems and multiple docking simulation packages to improve docking prediction reliability for network pharmacology
-
Hsin K-Y, Ghosh S, Kitano H. Combining machine learning systems and multiple docking simulation packages to improve docking prediction reliability for network pharmacology. PLoS One 2013, 8:e83922.
-
(2013)
PLoS One
, vol.8
, pp. e83922
-
-
Hsin, K.-Y.1
Ghosh, S.2
Kitano, H.3
-
58
-
-
80053313926
-
Support vector regression scoring of receptor-ligand complexes for rank-ordering and virtual screening of chemical libraries
-
Li L, Wang B, Meroueh SO. Support vector regression scoring of receptor-ligand complexes for rank-ordering and virtual screening of chemical libraries. J Chem Inf Model 2011, 51:2132-2138.
-
(2011)
J Chem Inf Model
, vol.51
, pp. 2132-2138
-
-
Li, L.1
Wang, B.2
Meroueh, S.O.3
-
59
-
-
84887106527
-
Computation of binding energies including their enthalpy and entropy components for protein-ligand complexes using support vector machines
-
Koppisetty CAK, Frank M, Kemp GJL, Nyholm P-G. Computation of binding energies including their enthalpy and entropy components for protein-ligand complexes using support vector machines. J Chem Inf Model 2013, 53:2559-2570.
-
(2013)
J Chem Inf Model
, vol.53
, pp. 2559-2570
-
-
Koppisetty, C.A.K.1
Frank, M.2
Kemp, G.J.L.3
Nyholm, P.-G.4
-
60
-
-
84868679998
-
Machine learning scoring functions based on random forest and support vector regression
-
Lecture Notes in Computer Science].
-
Ballester PJ. Machine learning scoring functions based on random forest and support vector regression. Lect Notes Bioinforma 2012, 7632:14-25. [Lecture Notes in Computer Science].
-
(2012)
Lect Notes Bioinforma
, vol.7632
, pp. 14-25
-
-
Ballester, P.J.1
-
61
-
-
84875428269
-
ID-score: a new empirical scoring function based on a comprehensive set of descriptors related to protein-ligand interactions
-
Li G-B, Yang L-L, Wang W-J, Li L-L, Yang S-Y. ID-score: a new empirical scoring function based on a comprehensive set of descriptors related to protein-ligand interactions. J Chem Inf Model 2013, 53:592-600.
-
(2013)
J Chem Inf Model
, vol.53
, pp. 592-600
-
-
Li, G.-B.1
Yang, L.-L.2
Wang, W.-J.3
Li, L.-L.4
Yang, S.-Y.5
-
62
-
-
84888606432
-
Binding affinity prediction for protein-ligand complexes based on β contacts and B factor
-
Liu Q, Kwoh CK, Li J. Binding affinity prediction for protein-ligand complexes based on β contacts and B factor. J Chem Inf Model 2013, 53:3076-3085.
-
(2013)
J Chem Inf Model
, vol.53
, pp. 3076-3085
-
-
Liu, Q.1
Kwoh, C.K.2
Li, J.3
-
63
-
-
84883250593
-
SFCscore(RF): a random forest-based scoring function for improved affinity prediction of protein-ligand complexes
-
Zilian D, Sotriffer CA. SFCscore(RF): a random forest-based scoring function for improved affinity prediction of protein-ligand complexes. J Chem Inf Model 2013, 53:1923-1933.
-
(2013)
J Chem Inf Model
, vol.53
, pp. 1923-1933
-
-
Zilian, D.1
Sotriffer, C.A.2
-
64
-
-
84897010735
-
Does a more precise chemical description of protein-ligand complexes lead to more accurate prediction of binding affinity?
-
Ballester PJ, Schreyer A, Blundell TL. Does a more precise chemical description of protein-ligand complexes lead to more accurate prediction of binding affinity? J Chem Inf Model 2014, 54:944-955.
-
(2014)
J Chem Inf Model
, vol.54
, pp. 944-955
-
-
Ballester, P.J.1
Schreyer, A.2
Blundell, T.L.3
-
65
-
-
82355186299
-
NNScore 2.0: a neural-network receptor-ligand scoring function
-
Durrant JD, McCammon JA. NNScore 2.0: a neural-network receptor-ligand scoring function. J Chem Inf Model 2011, 51:2897-2903.
-
(2011)
J Chem Inf Model
, vol.51
, pp. 2897-2903
-
-
Durrant, J.D.1
McCammon, J.A.2
-
66
-
-
84906829436
-
Substituting random forest for multiple linear regression improves binding affinity prediction of scoring functions: Cyscore as a case study
-
Li H, Leung K-S, Wong M-H, Ballester PJ. Substituting random forest for multiple linear regression improves binding affinity prediction of scoring functions: Cyscore as a case study. BMC Bioinformatics 2014, 15:291.
-
(2014)
BMC Bioinformatics
, vol.15
, pp. 291
-
-
Li, H.1
Leung, K.-S.2
Wong, M.-H.3
Ballester, P.J.4
-
67
-
-
79952178127
-
A machine learning-based method to improve docking scoring functions and its application to drug repurposing
-
Kinnings SL, Liu N, Tonge PJ, Jackson RM, Xie L, Bourne PE. A machine learning-based method to improve docking scoring functions and its application to drug repurposing. J Chem Inf Model 2011, 51:408-419.
-
(2011)
J Chem Inf Model
, vol.51
, pp. 408-419
-
-
Kinnings, S.L.1
Liu, N.2
Tonge, P.J.3
Jackson, R.M.4
Xie, L.5
Bourne, P.E.6
-
68
-
-
84927634713
-
A comparative assessment of predictive accuracies of conventional and machine learning scoring functions for protein-ligand binding affinity prediction
-
Ashtawy HM, Mahapatra NR. A comparative assessment of predictive accuracies of conventional and machine learning scoring functions for protein-ligand binding affinity prediction. IEEE/ACM Trans Comput Biol Bioinforma 2015, 12:335-347.
-
(2015)
IEEE/ACM Trans Comput Biol Bioinforma
, vol.12
, pp. 335-347
-
-
Ashtawy, H.M.1
Mahapatra, N.R.2
-
69
-
-
78649517318
-
Leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets
-
Kramer C, Gedeck P. Leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets. J Chem Inf Model 2010, 50:1961-1969.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 1961-1969
-
-
Kramer, C.1
Gedeck, P.2
-
70
-
-
80051984855
-
Comments on 'leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets': significance for the validation of scoring functions
-
Ballester PJ, Mitchell JBO. Comments on 'leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets': significance for the validation of scoring functions. J Chem Inf Model 2011, 51:1739-1741.
-
(2011)
J Chem Inf Model
, vol.51
, pp. 1739-1741
-
-
Ballester, P.J.1
Mitchell, J.B.O.2
-
71
-
-
84925496993
-
A comparative study of family-specific protein-ligand complex affinity prediction based on random forest approach
-
Wang Y, Guo Y, Kuang Q, Pu X, Ji Y, Zhang Z, Li M. A comparative study of family-specific protein-ligand complex affinity prediction based on random forest approach. J Comput Aided Mol Des 2015, 29:349-360.
-
(2015)
J Comput Aided Mol Des
, vol.29
, pp. 349-360
-
-
Wang, Y.1
Guo, Y.2
Kuang, Q.3
Pu, X.4
Ji, Y.5
Zhang, Z.6
Li, M.7
-
72
-
-
36749002607
-
A general approach for developing system-specific functions to score protein-ligand docked complexes using support vector inductive logic programming
-
Amini A, Shrimpton PJ, Muggleton SH, Sternberg MJE. A general approach for developing system-specific functions to score protein-ligand docked complexes using support vector inductive logic programming. Proteins Struct Funct Bioinforma 2007, 69:823-831.
-
(2007)
Proteins Struct Funct Bioinforma
, vol.69
, pp. 823-831
-
-
Amini, A.1
Shrimpton, P.J.2
Muggleton, S.H.3
Sternberg, M.J.E.4
-
73
-
-
34250892548
-
eHiTS: a new fast, exhaustive flexible ligand docking system
-
Zsoldos Z, Reid D, Simon A, Sadjad SB, Johnson AP. eHiTS: a new fast, exhaustive flexible ligand docking system. J Mol Graph Model 2007, 26:198-212.
-
(2007)
J Mol Graph Model
, vol.26
, pp. 198-212
-
-
Zsoldos, Z.1
Reid, D.2
Simon, A.3
Sadjad, S.B.4
Johnson, A.P.5
-
74
-
-
84893553641
-
Integrating docking scores, interaction profiles and molecular descriptors to improve the accuracy of molecular docking: toward the discovery of novel Akt1 inhibitors
-
Zhan W, Li D, Che J, Zhang L, Yang B, Hu Y, Liu T, Dong X. Integrating docking scores, interaction profiles and molecular descriptors to improve the accuracy of molecular docking: toward the discovery of novel Akt1 inhibitors. Eur J Med Chem 2014, 75:11-20.
-
(2014)
Eur J Med Chem
, vol.75
, pp. 11-20
-
-
Zhan, W.1
Li, D.2
Che, J.3
Zhang, L.4
Yang, B.5
Hu, Y.6
Liu, T.7
Dong, X.8
-
75
-
-
84880564425
-
Water network perturbation in ligand binding: adenosine A
-
Bortolato A, Tehan BG, Bodnarchuk MS, Essex JW, Mason JS. Water network perturbation in ligand binding: adenosine A. J Chem Inf Model 2013, 53:1700-1713.
-
(2013)
J Chem Inf Model
, vol.53
, pp. 1700-1713
-
-
Bortolato, A.1
Tehan, B.G.2
Bodnarchuk, M.S.3
Essex, J.W.4
Mason, J.S.5
-
76
-
-
0035478854
-
Random forests
-
Breiman L. Random forests. Mach Learn 2001, 45:5-32.
-
(2001)
Mach Learn
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
77
-
-
27444445346
-
PostDOCK: a structural, empirical approach to scoring protein ligand complexes
-
Springer C, Adalsteinsson H, Young MM, Kegelmeyer PW, Roe DC. 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
-
78
-
-
75749126524
-
Combining machine learning and pharmacophore-based interaction fingerprint for in silico screening
-
Sato T, Honma T, Yokoyama S. Combining machine learning and pharmacophore-based interaction fingerprint for in silico screening. J Chem Inf Model 2010, 50:170-185.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 170-185
-
-
Sato, T.1
Honma, T.2
Yokoyama, S.3
-
79
-
-
84862192766
-
ChEMBL: a large-scale bioactivity database for drug discovery
-
Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, et al. ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res 2011.
-
(2011)
Nucleic Acids Res
-
-
Gaulton, A.1
Bellis, L.J.2
Bento, A.P.3
Chambers, J.4
Davies, M.5
Hersey, A.6
Light, Y.7
McGlinchey, S.8
Michalovich, D.9
Al-Lazikani, B.10
-
80
-
-
78649386109
-
Exploiting PubChem for virtual screening
-
Xie X-Q. Exploiting PubChem for virtual screening. Expert Opin Drug Discov 2010, 5:1205-1220.
-
(2010)
Expert Opin Drug Discov
, vol.5
, pp. 1205-1220
-
-
Xie, X.-Q.1
-
81
-
-
70349932423
-
AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility
-
Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 2009, 30:2785-2791.
-
(2009)
J Comput Chem
, vol.30
, pp. 2785-2791
-
-
Morris, G.M.1
Huey, R.2
Lindstrom, W.3
Sanner, M.F.4
Belew, R.K.5
Goodsell, D.S.6
Olson, A.J.7
-
82
-
-
84880552522
-
Comparing neural-network scoring functions and the state of the art: applications to common library screening
-
Durrant JD, Friedman AJ, Rogers KE, McCammon JA. Comparing neural-network scoring functions and the state of the art: applications to common library screening. J Chem Inf Model 2013, 53:1726-1735.
-
(2013)
J Chem Inf Model
, vol.53
, pp. 1726-1735
-
-
Durrant, J.D.1
Friedman, A.J.2
Rogers, K.E.3
McCammon, J.A.4
-
83
-
-
79952178127
-
Correction to 'a machine learning-based method to improve docking scoring functions and its application to drug repurposing'
-
Kinnings SL, Liu N, Tonge PJ, Jackson RM, Xie L, Bourne PE. Correction to 'a machine learning-based method to improve docking scoring functions and its application to drug repurposing'. J Chem Inf Model 2011, 51:408-419.
-
(2011)
J Chem Inf Model
, vol.51
, pp. 408-419
-
-
Kinnings, S.L.1
Liu, N.2
Tonge, P.J.3
Jackson, R.M.4
Xie, L.5
Bourne, P.E.6
-
84
-
-
79955401050
-
Target-specific support vector machine scoring in structure-based virtual screening: computational validation, in vitro testing in kinases, and effects on lung cancer cell proliferation
-
Li L, Khanna M, Jo I, Wang F, Ashpole NM, Hudmon A, Meroueh SO. Target-specific support vector machine scoring in structure-based virtual screening: computational validation, in vitro testing in kinases, and effects on lung cancer cell proliferation. J Chem Inf Model 2011, 51:755-759.
-
(2011)
J Chem Inf Model
, vol.51
, pp. 755-759
-
-
Li, L.1
Khanna, M.2
Jo, I.3
Wang, F.4
Ashpole, N.M.5
Hudmon, A.6
Meroueh, S.O.7
-
85
-
-
84868556569
-
Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification
-
Ballester PJ, Mangold M, Howard NI, Robinson RLM, Abell C, Blumberger J, Mitchell JBO. Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification. J R Soc Interface 2012.
-
(2012)
J R Soc Interface
-
-
Ballester, P.J.1
Mangold, M.2
Howard, N.I.3
Robinson, R.L.M.4
Abell, C.5
Blumberger, J.6
Mitchell, J.B.O.7
-
86
-
-
36349009372
-
Ultrafast shape recognition for similarity search in molecular databases
-
Ballester PJ, Richards WG. Ultrafast shape recognition for similarity search in molecular databases. Proc Math Phys Eng Sci 2007, 463:1307-1321.
-
(2007)
Proc Math Phys Eng Sci
, vol.463
, pp. 1307-1321
-
-
Ballester, P.J.1
Richards, W.G.2
-
87
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
Jones G, Willett P, Glen RC, Leach AR, 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
-
88
-
-
84894639153
-
istar: A web platform for large-scale protein-ligand docking
-
Li H, Leung K-S, Ballester PJ, Wong M-H. istar: A web platform for large-scale protein-ligand docking. PLoS One 2014, 9:e85678.
-
(2014)
PLoS One
, vol.9
, pp. e85678
-
-
Li, H.1
Leung, K.-S.2
Ballester, P.J.3
Wong, M.-H.4
-
89
-
-
84864199587
-
ZINC: a free tool to discover chemistry for biology
-
Irwin JJ, Sterling T, Mysinger MM, Bolstad ES, Coleman RG. ZINC: a free tool to discover chemistry for biology. J Chem Inf Model 2012, 52:1757-1768.
-
(2012)
J Chem Inf Model
, vol.52
, pp. 1757-1768
-
-
Irwin, J.J.1
Sterling, T.2
Mysinger, M.M.3
Bolstad, E.S.4
Coleman, R.G.5
-
90
-
-
84873041650
-
Characterization of small molecule binding. I. Accurate identification of strong inhibitors in virtual screening
-
Ding B, Wang J, Li N, Wang W. Characterization of small molecule binding. I. Accurate identification of strong inhibitors in virtual screening. J Chem Inf Model 2013, 53:114-122.
-
(2013)
J Chem Inf Model
, vol.53
, pp. 114-122
-
-
Ding, B.1
Wang, J.2
Li, N.3
Wang, W.4
-
91
-
-
84945454057
-
The impact of docking pose generation error on the prediction of binding affinity
-
In: Switzerland: Springer
-
Li H, Leung K-S, Wong M-H, Ballester P. The impact of docking pose generation error on the prediction of binding affinity. In: Lecture Notes in Bioinformatics, vol. 8623. Switzerland: Springer; 2015.
-
(2015)
Lecture Notes in Bioinformatics
, vol.8623
-
-
Li, H.1
Leung, K.-S.2
Wong, M.-H.3
Ballester, P.4
-
92
-
-
84932194253
-
Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field
-
Wójcikowski M, Zielenkiewicz P, Siedlecki P. Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field. J Cheminform 2015, 7:26.
-
(2015)
J Cheminform
, vol.7
, pp. 26
-
-
Wójcikowski, M.1
Zielenkiewicz, P.2
Siedlecki, P.3
-
93
-
-
84896695700
-
Machine learning estimates of natural product conformational energies
-
Rupp M, Bauer MR, Wilcken R, Lange A, Reutlinger M, Boeckler FM, Schneider G. Machine learning estimates of natural product conformational energies. PLoS Comput Biol 2014, 10:e1003400.
-
(2014)
PLoS Comput Biol
, vol.10
, pp. e1003400
-
-
Rupp, M.1
Bauer, M.R.2
Wilcken, R.3
Lange, A.4
Reutlinger, M.5
Boeckler, F.M.6
Schneider, G.7
-
94
-
-
84939564287
-
Optimizing the affinity and specificity of ligand binding with the inclusion of solvation effect
-
Yan Z, Wang J. Optimizing the affinity and specificity of ligand binding with the inclusion of solvation effect. Proteins Struct Funct Bioinforma 2015.
-
(2015)
Proteins Struct Funct Bioinforma
-
-
Yan, Z.1
Wang, J.2
-
95
-
-
84902438255
-
Improved protein-ligand binding affinity prediction by using a curvature dependent surface area model
-
Cao Y, Li L. Improved protein-ligand binding affinity prediction by using a curvature dependent surface area model. Bioinformatics 2014, 30:1674-1680.
-
(2014)
Bioinformatics
, vol.30
, pp. 1674-1680
-
-
Cao, Y.1
Li, L.2
-
96
-
-
84865305788
-
Protein-protein binding affinity prediction based on an SVR ensemble
-
In: Huang D-S, Jiang C, Bevilacqua V, Figueroa J, eds. Berlin/Heidelberg: Springer;
-
Li X, Zhu M, Li X, Wang H-Q, Wang S. Protein-protein binding affinity prediction based on an SVR ensemble. In: Huang D-S, Jiang C, Bevilacqua V, Figueroa J, eds. Intelligent Computing Technology, vol. 7389. Berlin/Heidelberg: Springer; 2012, 145-151.
-
(2012)
Intelligent Computing Technology
, vol.7389
, pp. 145-151
-
-
Li, X.1
Zhu, M.2
Li, X.3
Wang, H.-Q.4
Wang, S.5
-
97
-
-
84880698928
-
Optimization of molecular docking scores with support vector rank regression
-
Wang W, He W, Zhou X, Chen X. Optimization of molecular docking scores with support vector rank regression. Proteins Struct Funct Bioinforma 2013, 81:1386-1398.
-
(2013)
Proteins Struct Funct Bioinforma
, vol.81
, pp. 1386-1398
-
-
Wang, W.1
He, W.2
Zhou, X.3
Chen, X.4
-
98
-
-
84938280812
-
Low-quality structural and interaction data improves binding affinity prediction via random forest
-
Li H, Leung K-S, Wong M-H, Ballester P. Low-quality structural and interaction data improves binding affinity prediction via random forest. Molecules 2015, 20:10947-10962.
-
(2015)
Molecules
, vol.20
, pp. 10947-10962
-
-
Li, H.1
Leung, K.-S.2
Wong, M.-H.3
Ballester, P.4
-
99
-
-
68149160790
-
Predicting the predictability: a unified approach to the applicability domain problem of QSAR models
-
Dragos H, Gilles M, Alexandre V. Predicting the predictability: a unified approach to the applicability domain problem of QSAR models. J Chem Inf Model 2009, 49:1762-1776.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 1762-1776
-
-
Dragos, H.1
Gilles, M.2
Alexandre, V.3
-
100
-
-
84888603687
-
Using random forest to model the domain applicability of another random forest model
-
Sheridan RP. Using random forest to model the domain applicability of another random forest model. J Chem Inf Model 2013, 53:2837-2850.
-
(2013)
J Chem Inf Model
, vol.53
, pp. 2837-2850
-
-
Sheridan, R.P.1
-
101
-
-
84894661270
-
Assessment of machine learning reliability methods for quantifying the applicability domain of QSAR regression models
-
Toplak M, Močnik R, Polajnar M, Bosnić Z, Carlsson L, Hasselgren C, Demšar J, Boyer S, Zupan B, Stålring J. Assessment of machine learning reliability methods for quantifying the applicability domain of QSAR regression models. J Chem Inf Model 2014, 54:431-441.
-
(2014)
J Chem Inf Model
, vol.54
, pp. 431-441
-
-
Toplak, M.1
Močnik, R.2
Polajnar, M.3
Bosnić, Z.4
Carlsson, L.5
Hasselgren, C.6
Demšar, J.7
Boyer, S.8
Zupan, B.9
Stålring, J.10
-
102
-
-
84874425485
-
Discovery of novel antimalarial compounds enabled by QSAR-based virtual screening
-
Zhang L, Fourches D, Sedykh A, Zhu H, Golbraikh A, Ekins S, Clark J, Connelly MC, Sigal M, Hodges D, et al. Discovery of novel antimalarial compounds enabled by QSAR-based virtual screening. J Chem Inf Model 2012.
-
(2012)
J Chem Inf Model
-
-
Zhang, L.1
Fourches, D.2
Sedykh, A.3
Zhu, H.4
Golbraikh, A.5
Ekins, S.6
Clark, J.7
Connelly, M.C.8
Sigal, M.9
Hodges, D.10
-
103
-
-
84901364194
-
Chemical, target, and bioactive properties of allosteric modulation
-
Van Westen GJP, Gaulton A, Overington JP. Chemical, target, and bioactive properties of allosteric modulation. PLoS Comput Biol 2014, 10:e1003559.
-
(2014)
PLoS Comput Biol
, vol.10
, pp. e1003559
-
-
Van Westen, G.J.P.1
Gaulton, A.2
Overington, J.P.3
-
104
-
-
77952732009
-
Bioisosteric replacement and scaffold hopping in lead generation and optimization
-
Langdon SR, Ertl P, Brown N. Bioisosteric replacement and scaffold hopping in lead generation and optimization. Mol Inform 2010, 29:366-385.
-
(2010)
Mol Inform
, vol.29
, pp. 366-385
-
-
Langdon, S.R.1
Ertl, P.2
Brown, N.3
-
106
-
-
80051551297
-
Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information
-
Sushko I, Novotarskyi S, Körner R, Pandey AK, Rupp M, Teetz W, Brandmaier S, Abdelaziz A, Prokopenko VV, Tanchuk VY, et al. Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. J Comput Aided Mol Des 2011, 25:533-554.
-
(2011)
J Comput Aided Mol Des
, vol.25
, pp. 533-554
-
-
Sushko, I.1
Novotarskyi, S.2
Körner, R.3
Pandey, A.K.4
Rupp, M.5
Teetz, W.6
Brandmaier, S.7
Abdelaziz, A.8
Prokopenko, V.V.9
Tanchuk, V.Y.10
-
107
-
-
84875618780
-
aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction
-
Pires DE V, de Melo-Minardi RC, da Silveira CH, Campos FF, Meira W. aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction. Bioinformatics 2013, 29:855-861.
-
(2013)
Bioinformatics
, vol.29
, pp. 855-861
-
-
Pires, D.E.V.1
de Melo-Minardi, R.C.2
da Silveira, C.H.3
Campos, F.F.4
Meira, W.5
-
108
-
-
34250628103
-
Principles of QSAR models validation: internal and external
-
Gramatica P. Principles of QSAR models validation: internal and external. QSAR Comb Sci 2007, 26:694-701.
-
(2007)
QSAR Comb Sci
, vol.26
, pp. 694-701
-
-
Gramatica, P.1
-
109
-
-
84920496470
-
Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects
-
Cortés-Ciriano I, Ain QU, Subramanian V, Lenselink EB, Méndez-Lucio O, IJzerman AP, Wohlfahrt G, Prusis P, Malliavin TE, van Westen GJP, et al. Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects. Med Chem Commun 2015, 6:24-50.
-
(2015)
Med Chem Commun
, vol.6
, pp. 24-50
-
-
Cortés-Ciriano, I.1
Ain, Q.U.2
Subramanian, V.3
Lenselink, E.B.4
Méndez-Lucio, O.5
IJzerman, A.P.6
Wohlfahrt, G.7
Prusis, P.8
Malliavin, T.E.9
van Westen, G.J.P.10
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