-
1
-
-
40349087133
-
Towards the development of universal, fast and highly accurate docking/scoring methods: A long way to go
-
Moitessier, N., et al.: Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. Br. J. Pharmacol. 153, S7-S26 (2008)
-
(2008)
Br. J. Pharmacol.
, vol.153
-
-
Moitessier, N.1
-
2
-
-
33750898990
-
Molecular mechanics methods for predicting protein-ligand binding
-
Huang, N., et al.: Molecular mechanics methods for predicting protein-ligand binding. Phys. Chem. Chem. Phys. 8, 5166-5177 (2006)
-
(2006)
Phys. Chem. Chem. Phys.
, vol.8
, pp. 5166-5177
-
-
Huang, N.1
-
3
-
-
0000823044
-
BLEEP - Potential of mean force describing protein-ligand interactions: I. Generating potential
-
Mitchell, J.B.O., et al.: BLEEP - potential of mean force describing protein-ligand interactions: I. Generating potential. J. Comput. Chem. 20, 1165-1176 (1999)
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 1165-1176
-
-
Mitchell, J.B.O.1
-
4
-
-
60349109713
-
Computational evaluation of protein-small molecule binding
-
Guvench, O., MacKerell Jr., A.D.: Computational evaluation of protein-small molecule binding. Curr. Opin. Struct. Biol. 19, 56-61 (2009)
-
(2009)
Curr. Opin. Struct. Biol.
, vol.19
, pp. 56-61
-
-
Guvench, O.1
MacKerell Jr., A.D.2
-
5
-
-
77955663115
-
Prediction of protein - Ligand binding affinity by free energy simulations: Assumptions, pitfalls and expectations
-
Michel, J., Essex, J.W.: Prediction of protein - ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations. J. Comput. Aided Mol. Des. 24, 639-658 (2010)
-
(2010)
J. Comput. Aided Mol. Des.
, vol.24
, pp. 639-658
-
-
Michel, J.1
Essex, J.W.2
-
6
-
-
77952825581
-
A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking
-
Ballester, P.J., Mitchell, J.B.O.: A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking. Bioinformatics 26, 1169-1175 (2010)
-
(2010)
Bioinformatics
, vol.26
, pp. 1169-1175
-
-
Ballester, P.J.1
Mitchell, J.B.O.2
-
7
-
-
84857456082
-
Limiting assumptions in structure-based design: Binding entropy
-
Marshall, G.R.: Limiting assumptions in structure-based design: binding entropy. J. Comput. Aided Mol. Des. 26(1), 3-8 (2012)
-
(2012)
J. Comput. Aided Mol. Des.
, vol.26
, Issue.1
, pp. 3-8
-
-
Marshall, G.R.1
-
8
-
-
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. 397, 1042-1054 (2010)
-
(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
-
9
-
-
79960880477
-
Definition of the hydrogen bond (IUPAC Recommendations 2011)
-
Arunan, E., et al.: Definition of the hydrogen bond (IUPAC Recommendations 2011). Pure and Applied Chemistry 83, 1637-1641 (2011)
-
(2011)
Pure and Applied Chemistry
, vol.83
, pp. 1637-1641
-
-
Arunan, E.1
-
10
-
-
81055130316
-
Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase
-
Snyder, P.W., et al.: Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase. Proceedings of the National Academy of Sciences 108, 17889-17894 (2011)
-
(2011)
Proceedings of the National Academy of Sciences
, vol.108
, pp. 17889-17894
-
-
Snyder, P.W.1
-
11
-
-
77956166424
-
Docking to Erlotinib Off-Targets Leads to Inhibitors of Lung Cancer Cell Proliferation with Suitable in Vitro Pharmacokinetics
-
Li, L., Li, J., Khanna, M., Jo, I., Baird, J.P., Meroueh, S.O.: Docking to Erlotinib Off-Targets Leads to Inhibitors of Lung Cancer Cell Proliferation with Suitable in Vitro Pharmacokinetics. ACS Med. Chem. Lett. 1(5), 229-233 (2010)
-
(2010)
ACS Med. Chem. Lett.
, vol.1
, Issue.5
, pp. 229-233
-
-
Li, L.1
Li, J.2
Khanna, M.3
Jo, I.4
Baird, J.P.5
Meroueh, S.O.6
-
12
-
-
77958585233
-
NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein-Ligand Complexes
-
Durrant, J.D., McCammon, J.A.: NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein-Ligand Complexes. J. Chem. Inf. Model. 50(10), 1865-1871 (2010)
-
(2010)
J. Chem. Inf. Model.
, vol.50
, Issue.10
, pp. 1865-1871
-
-
Durrant, J.D.1
McCammon, J.A.2
-
13
-
-
80051984855
-
'Leave-Cluster-Out Cross-Validation is appropriate for scoring functions derived from diverse protein data sets': Significance for the validation of scoring functions
-
Comments on
-
Ballester, P.J., Mitchell, J.B.O.: 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. 51, 1739-1741 (2011)
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 1739-1741
-
-
Ballester, P.J.1
Mitchell, J.B.O.2
-
14
-
-
84862795414
-
Structure-Based Virtual Screening for Drug Discovery: A Problem-Centric Review
-
Cheng, T., Li, Q., Zhou, Z., Wang, Y., Bryant, S.H.: Structure-Based Virtual Screening for Drug Discovery: a Problem-Centric Review. The AAPS Journal 14(1), 133-141 (2012)
-
(2012)
The AAPS Journal
, vol.14
, Issue.1
, pp. 133-141
-
-
Cheng, T.1
Li, Q.2
Zhou, Z.3
Wang, Y.4
Bryant, S.H.5
-
15
-
-
79952178127
-
A Machine Learning-Based Method to Improve Docking Scoring Functions and its Application to Drug Repurposing
-
Kinnings, S.L., Liu, N., Tonge, P.J., Jackson, R.M., Xie, L., Bourne, P.E.: A Machine Learning-Based Method to Improve Docking Scoring Functions and its Application to Drug Repurposing. J. Chem. Inf. Model. 51, 408-419 (2011)
-
(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
-
16
-
-
77649229098
-
Binding Affinity Prediction with Property-Encoded Shape Distribution Signatures
-
Das, S., Krein, M.P., Breneman, C.M.: Binding Affinity Prediction with Property-Encoded Shape Distribution Signatures. J. Chem. Inf. Model. 50, 298-308 (2010)
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 298-308
-
-
Das, S.1
Krein, M.P.2
Breneman, C.M.3
-
17
-
-
80053313926
-
Support Vector Regression Scoring of Receptor-Ligand Complexes for Rank-Ordering and Virtual Screening of Chemical Libraries
-
Li, L., Wang, B., Meroueh, S.O.: Support Vector Regression Scoring of Receptor-Ligand Complexes for Rank-Ordering and Virtual Screening of Chemical Libraries. J. Chem. Inf. Model. 51, 2132-2138 (2011)
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 2132-2138
-
-
Li, L.1
Wang, B.2
Meroueh, S.O.3
-
18
-
-
82355186299
-
NNScore 2.0: A Neural-Network Receptor-Ligand Scoring Function
-
Durrant, J.D., McCammon, J.A.: NNScore 2.0: A Neural-Network Receptor-Ligand Scoring Function. J. Chem. Inf. Model. 51(11), 2897-2903 (2011)
-
(2011)
J. Chem. Inf. Model.
, vol.51
, Issue.11
, pp. 2897-2903
-
-
Durrant, J.D.1
McCammon, J.A.2
-
19
-
-
0035478854
-
Random Forests
-
Breiman, L.: Random Forests. Mach. Learn. 45, 5-32 (2001)
-
(2001)
Mach. Learn.
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
21
-
-
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.: 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)
-
(2007)
Proteins
, vol.69
, pp. 823-831
-
-
Amini, A.1
-
23
-
-
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. 49, 1079-1093 (2009)
-
(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
-
24
-
-
37349097759
-
y-Randomization and its variants in QSPR/QSAR
-
Rucker, C., Rucker, G., Meringer, M.: y-Randomization and its variants in QSPR/QSAR. J. Chem. Inf. Model. 47, 2345-2357 (2007)
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 2345-2357
-
-
Rucker, C.1
Rucker, G.2
Meringer, M.3
-
26
-
-
52249113723
-
SFCscore: Scoring functions for affinity prediction of protein-ligand complexes
-
Sotriffer, C.A., Sanschagrin, P., Matter, H., Klebe, G.: SFCscore: scoring functions for affinity prediction of protein-ligand complexes. Proteins 73, 395-419 (2008)
-
(2008)
Proteins
, vol.73
, pp. 395-419
-
-
Sotriffer, C.A.1
Sanschagrin, P.2
Matter, H.3
Klebe, G.4
-
27
-
-
34250892548
-
eHiTS: A new fast, exhaustive flexible ligand docking system
-
Zsoldos, Z., Reid, D., Simon, A., Sadjad, S.B., Johnson, A.P.: eHiTS: a new fast, exhaustive flexible ligand docking system. J. Mol. Graph. Model. 26, 198-212 (2007)
-
(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
-
28
-
-
0002714543
-
Making large-Scale SVM Learning Practical
-
Schölkopf, B., Burges, C., Smola, A. (eds.) MIT Press
-
Joachims, T.: Making large-Scale SVM Learning Practical. In: Schölkopf, B., Burges, C., Smola, A. (eds.) Advances in Kernel Methods - Support Vector Learning. MIT Press (1999)
-
(1999)
Advances in Kernel Methods - Support Vector Learning
-
-
Joachims, T.1
-
29
-
-
26444479778
-
Optimization by simulated annealing
-
Kirkpatrick, S.C., Gelatt, D., Vecchi, M.P.: Optimization by simulated annealing. Science 220, 671-680 (1983)
-
(1983)
Science
, vol.220
, pp. 671-680
-
-
Kirkpatrick, S.C.1
Gelatt, D.2
Vecchi, M.P.3
-
31
-
-
84868706764
-
-
last accessed November 2, 2011
-
CSAR, http://www.csardock.org (last accessed November 2, 2011).
-
-
-
-
32
-
-
84859746909
-
-
last accessed November 2, 2011
-
The PDBbind database, http://www.pdbbind-cn.org/ (last accessed November 2, 2011).
-
The PDBbind Database
-
-
-
33
-
-
0033954256
-
The Protein Data Bank
-
Berman, H.M., et al.: The Protein Data Bank. Nucleic Acids Res. 28, 235-242 (2000)
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
|