-
1
-
-
0042353897
-
Molecular Recognition and Docking Algorithms
-
Brooijmans, N.; Kuntz, I. D. Molecular Recognition and Docking Algorithms Annu. Rev. Biophys. Biomol. Struct. 2003, 32, 335-373 10.1146/annurev.biophys.32.110601.142532
-
(2003)
Annu. Rev. Biophys. Biomol. Struct.
, vol.32
, pp. 335-373
-
-
Brooijmans, N.1
Kuntz, I.D.2
-
2
-
-
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 Nat. Rev. Drug Discovery 2004, 3, 935-949 10.1038/nrd1549
-
(2004)
Nat. Rev. Drug Discovery
, vol.3
, pp. 935-949
-
-
Kitchen, D.B.1
Decornez, H.2
Furr, J.R.3
Bajorath, J.4
-
3
-
-
77957899529
-
Advances and Challenges in Protein-Ligand Docking
-
Huang, S.-Y.; Zou, X. Advances and Challenges in Protein-Ligand Docking Int. J. Mol. Sci. 2010, 11, 3016-3034 10.3390/ijms11083016
-
(2010)
Int. J. Mol. Sci.
, vol.11
, pp. 3016-3034
-
-
Huang, S.-Y.1
Zou, X.2
-
4
-
-
77957898063
-
Scoring Functions and Their Evaluation Methods for Protein-Ligand Docking: Recent Advances and Future Directions
-
Huang, S.-Y.; Grinter, S. Z.; 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 10.1039/c0cp00151a
-
(2010)
Phys. Chem. Chem. Phys.
, vol.12
, pp. 12899-12908
-
-
Huang, S.-Y.1
Grinter, S.Z.2
Zou, X.3
-
5
-
-
84904819424
-
Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-based Drug Design
-
Grinter, S. Z.; Zou, X. Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-based Drug Design Molecules 2014, 19, 10150-10176 10.3390/molecules190710150
-
(2014)
Molecules
, vol.19
, pp. 10150-10176
-
-
Grinter, S.Z.1
Zou, X.2
-
6
-
-
80053333972
-
CSAR Benchmark Exercise of 2010: Selection of the Protein-Ligand Complexes
-
Dunbar, J. B., Jr; Smith, R. D.; Yang, C.-Y.; Ung, P. M.-U.; Lexa, K. W.; Khazanov, N. A.; Stuckey, J. A.; Wang, S.; Carlson, H. A. CSAR Benchmark Exercise of 2010: Selection of the Protein-Ligand Complexes J. Chem. Inf. Model. 2011, 51, 2036-2046 10.1021/ci200082t
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 2036-2046
-
-
Dunbar, J.B.1
Smith, R.D.2
Yang, C.-Y.3
Ung, P.M.-U.4
Lexa, K.W.5
Khazanov, N.A.6
Stuckey, J.A.7
Wang, S.8
Carlson, H.A.9
-
7
-
-
84883209345
-
CSAR Benchmark Exercise 2011-2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series
-
Damm-Ganamet, K. L.; Smith, R. D.; Dunbar, J. B., Jr; Stuckey, J. A.; Carlson, H. A. CSAR Benchmark Exercise 2011-2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series J. Chem. Inf. Model. 2013, 53, 1853-1870 10.1021/ci400025f
-
(2013)
J. Chem. Inf. Model.
, vol.53
, pp. 1853-1870
-
-
Damm-Ganamet, K.L.1
Smith, R.D.2
Dunbar, J.B.3
Stuckey, J.A.4
Carlson, H.A.5
-
8
-
-
84883227058
-
CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys
-
Dunbar, J. B., Jr; Smith, R. D.; Damm-Ganamet, K. L.; Ahmed, A.; Esposito, E. X.; Delproposto, J.; Chinnaswamy, K.; Kang, Y.-N.; Kubish, G.; Gestwicki, J. E.; Stuckey, J. A.; Carlson, H. A. CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys J. Chem. Inf. Model. 2013, 53, 1842-1852 10.1021/ci4000486
-
(2013)
J. Chem. Inf. Model.
, vol.53
, pp. 1842-1852
-
-
Dunbar, J.B.1
Smith, R.D.2
Damm-Ganamet, K.L.3
Ahmed, A.4
Esposito, E.X.5
Delproposto, J.6
Chinnaswamy, K.7
Kang, Y.-N.8
Kubish, G.9
Gestwicki, J.E.10
Stuckey, J.A.11
Carlson, H.A.12
-
9
-
-
84884166196
-
Computational Design of Ligand-Binding Proteins with High Affinity and Selectivity
-
Tinberg, C. E.; Khare, S. D.; Dou, J.; Doyle, L.; Nelson, J. W.; Schena, A.; Jankowski, W.; Kalodimos, C. G.; Johnsson, K.; Stoddard, B. L.; Baker, D. Computational Design of Ligand-Binding Proteins with High Affinity and Selectivity Nature 2013, 501, 212-216 10.1038/nature12443
-
(2013)
Nature
, vol.501
, pp. 212-216
-
-
Tinberg, C.E.1
Khare, S.D.2
Dou, J.3
Doyle, L.4
Nelson, J.W.5
Schena, A.6
Jankowski, W.7
Kalodimos, C.G.8
Johnsson, K.9
Stoddard, B.L.10
Baker, D.11
-
10
-
-
33750555073
-
An Iterative Knowledge-based Scoring Function to Predict Protein-Ligand Interactions: I. Derivation of Interaction Potentials
-
Huang, S.-Y.; Zou, X. An Iterative Knowledge-based Scoring Function to Predict Protein-Ligand Interactions: I. Derivation of Interaction Potentials J. Comput. Chem. 2006, 27, 1866-1875 10.1002/jcc.20504
-
(2006)
J. Comput. Chem.
, vol.27
, pp. 1866-1875
-
-
Huang, S.-Y.1
Zou, X.2
-
11
-
-
33750574927
-
An Iterative Knowledge-based Scoring Function to Predict Protein-Ligand Interactions: II. Validation of the Scoring Function
-
Huang, S.-Y.; Zou, X. An Iterative Knowledge-based Scoring Function to Predict Protein-Ligand Interactions: II. Validation of the Scoring Function J. Comput. Chem. 2006, 27, 1876-1882 10.1002/jcc.20505
-
(2006)
J. Comput. Chem.
, vol.27
, pp. 1876-1882
-
-
Huang, S.-Y.1
Zou, X.2
-
12
-
-
80053297657
-
Scoring and Lessons Learned with the CSAR Benchmark Using an Improved Iterative Knowledge-based Scoring Function
-
Huang, S.-Y.; Zou, X. Scoring and Lessons Learned with the CSAR Benchmark Using an Improved Iterative Knowledge-based Scoring Function J. Chem. Inf. Model. 2011, 51, 2097-2106 10.1021/ci2000727
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 2097-2106
-
-
Huang, S.-Y.1
Zou, X.2
-
13
-
-
84883240307
-
Automated Large-Scale File Preparation, Docking, and Scoring: Evaluation of ITScore and STScore Using the 2012 Community Structure-Activity Resource Benchmark
-
Grinter, S. Z.; Yan, C.; Huang, S.-Y.; Jiang, L.; Zou, X. Automated Large-Scale File Preparation, Docking, and Scoring: Evaluation of ITScore and STScore Using the 2012 Community Structure-Activity Resource Benchmark J. Chem. Inf. Model. 2013, 53, 1905-1914 10.1021/ci400045v
-
(2013)
J. Chem. Inf. Model.
, vol.53
, pp. 1905-1914
-
-
Grinter, S.Z.1
Yan, C.2
Huang, S.-Y.3
Jiang, L.4
Zou, X.5
-
14
-
-
20444422149
-
The PDBbind Database: Methodologies and Updates
-
Wang, R.; Fang, X.; Lu, Y.; Yang, C.-Y.; Wang, S. The PDBbind Database: Methodologies and Updates J. Med. Chem. 2005, 48, 4111-4119 10.1021/jm048957q
-
(2005)
J. Med. Chem.
, vol.48
, pp. 4111-4119
-
-
Wang, R.1
Fang, X.2
Lu, Y.3
Yang, C.-Y.4
Wang, S.5
-
15
-
-
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 10.1021/ci9000053
-
(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
-
16
-
-
76149120388
-
AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading
-
Trott, O.; Olson, A. J. 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 10.1002/jcc.21334
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 455-461
-
-
Trott, O.1
Olson, A.J.2
-
17
-
-
33846000313
-
Ensemble Docking of Multiple Protein Structures: Considering Protein Structural Variations in Molecular Docking
-
Huang, S.-Y.; Zou, X. Ensemble Docking of Multiple Protein Structures: Considering Protein Structural Variations in Molecular Docking Proteins: Struct., Funct., Genet. 2007, 66, 399-421 10.1002/prot.21214
-
(2007)
Proteins: Struct., Funct., Genet.
, vol.66
, pp. 399-421
-
-
Huang, S.-Y.1
Zou, X.2
-
18
-
-
77951986384
-
Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database
-
Hawkins, P. C.; Skillman, A. G.; Warren, G. L.; Ellingson, B. A.; Stahl, M. T. Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database J. Chem. Inf. Model. 2010, 50, 572-584 10.1021/ci100031x
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 572-584
-
-
Hawkins, P.C.1
Skillman, A.G.2
Warren, G.L.3
Ellingson, B.A.4
Stahl, M.T.5
-
19
-
-
84869987609
-
Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures
-
Hawkins, P. C.; Nicholls, A. Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures J. Chem. Inf. Model. 2012, 52, 2919-2936 10.1021/ci300314k
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 2919-2936
-
-
Hawkins, P.C.1
Nicholls, A.2
-
20
-
-
66449110287
-
DOCK 6: Combining Techniques to Model RNA-Small Molecule Complexes
-
Lang, P. T.; Brozell, S. R.; Mukherjee, S.; Pettersen, E. F.; Meng, E. C.; Thomas, V.; Rizzo, R. C.; Case, D. A.; James, T. L.; Kuntz, I. D. DOCK 6: Combining Techniques to Model RNA-Small Molecule Complexes RNA 2009, 15, 1219-1230 10.1261/rna.1563609
-
(2009)
RNA
, vol.15
, pp. 1219-1230
-
-
Lang, P.T.1
Brozell, S.R.2
Mukherjee, S.3
Pettersen, E.F.4
Meng, E.C.5
Thomas, V.6
Rizzo, R.C.7
Case, D.A.8
James, T.L.9
Kuntz, I.D.10
-
21
-
-
0000238336
-
A Simplex Method for Function Minimization
-
Nelder, J. A.; Mead, R. A Simplex Method for Function Minimization Comput. J. 1965, 7, 308-313 10.1093/comjnl/7.4.308
-
(1965)
Comput. J.
, vol.7
, pp. 308-313
-
-
Nelder, J.A.1
Mead, R.2
-
22
-
-
4444221565
-
UCSF Chimera - A Visualization System for Exploratory Research and Analysis
-
Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. UCSF Chimera-A Visualization System for Exploratory Research and Analysis J. Comput. Chem. 2004, 25, 1605-1612 10.1002/jcc.20084
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
23
-
-
84923089768
-
-
The Graph-Tool Python Library. Figshare
-
Peixoto, T. P. The Graph-Tool Python Library. Figshare 2014, http://dx.doi.org/10.6084/m9.figshare.1164194.
-
(2014)
-
-
Peixoto, T.P.1
|