-
1
-
-
33748276474
-
Protein-ligand docking: Current status and future challenges
-
Sousa, S. F.; Fernandes, P. A.; Ramos, M. J. Protein-ligand docking: Current status and future challenges Proteins: Struct., Funct., Genet. 2006, 65, 15-26 10.1002/prot.21082
-
(2006)
Proteins: Struct., Funct., Genet.
, vol.65
, pp. 15-26
-
-
Sousa, S.F.1
Fernandes, P.A.2
Ramos, M.J.3
-
2
-
-
0347755444
-
Predicting Molecular Interactions in silico: II. Protein-Protein and Protein-Drug Docking
-
Schneidman-Duhovny, D.; Nussinov, R.; Wolfson, H. J. Predicting Molecular Interactions in silico: II. Protein-Protein and Protein-Drug Docking Curr. Med. Chem. 2004, 11, 91-107 10.2174/0929867043456223
-
(2004)
Curr. Med. Chem.
, vol.11
, pp. 91-107
-
-
Schneidman-Duhovny, D.1
Nussinov, R.2
Wolfson, H.J.3
-
3
-
-
80053177770
-
LigDockCSA: Protein-ligand docking using conformational space annealing
-
Shin, W.-H.; Heo, L.; Lee, J.; Ko, J.; Seok, C.; Lee, J. LigDockCSA: protein-ligand docking using conformational space annealing J. Comput. Chem. 2011, 32, 3226-3232 10.1002/jcc.21905
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 3226-3232
-
-
Shin, W.-H.1
Heo, L.2
Lee, J.3
Ko, J.4
Seok, C.5
Lee, J.6
-
4
-
-
84871604119
-
GalaxyDock: Protein-Ligand Docking with Flexible Protein Side-chains
-
Shin, W.-H.; Seok, C. GalaxyDock: Protein-Ligand Docking with Flexible Protein Side-chains J. Chem. Inf. Model. 2012, 52, 3225-3232 10.1021/ci300342z
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 3225-3232
-
-
Shin, W.-H.1
Seok, C.2
-
5
-
-
84885660146
-
GalaxyDock2: Protein-ligand docking using beta-complex and global optimization
-
Shin, W.-H.; Kim, J.-K.; Kim, D.-S.; Seok, C. GalaxyDock2: Protein-ligand docking using beta-complex and global optimization J. Comput. Chem. 2013, 34, 2647-2656 10.1002/jcc.23438
-
(2013)
J. Comput. Chem.
, vol.34
, pp. 2647-2656
-
-
Shin, W.-H.1
Kim, J.-K.2
Kim, D.-S.3
Seok, C.4
-
6
-
-
0001176785
-
New Optimization Method for Conformational Energy Calculations on Polypeptides: Conformational Space Annealing
-
Lee, J.; Scheraga, H. A.; Rackovsky, S. New Optimization Method for Conformational Energy Calculations on Polypeptides: Conformational Space Annealing J. Comput. Chem. 1997, 18, 1222-1232 10.1002/(SICI)1096-987X(19970715)18:9<1222::AID-JCC10>3.0.CO;2-7
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 1222-1232
-
-
Lee, J.1
Scheraga, H.A.2
Rackovsky, S.3
-
7
-
-
11644261806
-
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
-
Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function J. Comput. Chem. 1998, 19, 1639-1662 10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B
-
(1998)
J. Comput. Chem.
, vol.19
, pp. 1639-1662
-
-
Morris, G.M.1
Goodsell, D.S.2
Halliday, R.S.3
Huey, R.4
Hart, W.E.5
Belew, R.K.6
Olson, A.J.7
-
8
-
-
0029294584
-
Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming
-
Gehlhaar, D. K.; Verkhivker, G. M.; Rejto, P. A.; Sherman, C. J.; Fogel, D. R.; Fogel, L. J.; Freer, S. T. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming Chem. Biol. 1995, 2, 317-324 10.1016/1074-5521(95)90050-0
-
(1995)
Chem. Biol.
, vol.2
, pp. 317-324
-
-
Gehlhaar, D.K.1
Verkhivker, G.M.2
Rejto, P.A.3
Sherman, C.J.4
Fogel, D.R.5
Fogel, L.J.6
Freer, S.T.7
-
9
-
-
84913601869
-
Prediction of Protein Structure and Interaction by GALAXY protein modeling programs
-
Shin, W.-H.; Lee, G. R.; Heo, L.; Lee, H.; Seok, C. Prediction of Protein Structure and Interaction by GALAXY protein modeling programs Bio Design 2014, 2, 1-11
-
(2014)
Bio Design
, vol.2
, pp. 1-11
-
-
Shin, W.-H.1
Lee, G.R.2
Heo, L.3
Lee, H.4
Seok, C.5
-
10
-
-
0029224965
-
A genetic algorithm for flowshop sequencing
-
Reeves, C. R. A genetic algorithm for flowshop sequencing Comput. Oper. Res. 1995, 22, 5-13 10.1016/0305-0548(93)E0014-K
-
(1995)
Comput. Oper. Res.
, vol.22
, pp. 5-13
-
-
Reeves, C.R.1
-
11
-
-
77955569416
-
Three-dimensional beta-shapes and beta-complexes via quasi-triangulation
-
Kim, D.-S.; Cho, Y.; Sugihara, K.; Ryu, J.; Kim, D. Three-dimensional beta-shapes and beta-complexes via quasi-triangulation Comput. -Aided Des. 2010, 42, 911-929 10.1016/j.cad.2010.06.004
-
(2010)
Comput. -Aided Des.
, vol.42
, pp. 911-929
-
-
Kim, D.-S.1
Cho, Y.2
Sugihara, K.3
Ryu, J.4
Kim, D.5
-
12
-
-
33847347192
-
Diverse, High-Quality Test Set for the Validation of Protein-Ligand Docking Performance
-
Hartshorn, M. J.; Verdonk, M. L.; Chessari, G.; Brewerton, S. C.; Mooij, W. T. M.; Mortenson, P. N.; Murray, C. W. Diverse, High-Quality Test Set for the Validation of Protein-Ligand Docking Performance J. Med. Chem. 2007, 50, 726-741 10.1021/jm061277y
-
(2007)
J. Med. Chem.
, vol.50
, pp. 726-741
-
-
Hartshorn, M.J.1
Verdonk, M.L.2
Chessari, G.3
Brewerton, S.C.4
Mooij, W.T.M.5
Mortenson, P.N.6
Murray, C.W.7
-
13
-
-
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
-
14
-
-
33644873904
-
AffinDB: A freely accessible database of affinities for protein-ligand complexes from the PDB
-
Block, P.; Sotriffer, C. A.; Dramburg, I.; Klebe, G. AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB Nucleic Acids Res. 2006, 34, D522-D526 10.1093/nar/gkj039
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. D522-D526
-
-
Block, P.1
Sotriffer, C.A.2
Dramburg, I.3
Klebe, G.4
-
15
-
-
33947716119
-
A semiempirical free energy with charge-based desolvation
-
Huey, R.; Morris, G. M.; Olson, A. J.; Goodsell, D. S. A semiempirical free energy with charge-based desolvation J. Comput. Chem. 2007, 28, 1145-1152 10.1002/jcc.20634
-
(2007)
J. Comput. Chem.
, vol.28
, pp. 1145-1152
-
-
Huey, R.1
Morris, G.M.2
Olson, A.J.3
Goodsell, D.S.4
-
16
-
-
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
-
17
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
Söding, J. Protein homology detection by HMM-HMM comparison Bioinformatics 2005, 21, 951-960 10.1093/bioinformatics/bti125
-
(2005)
Bioinformatics
, vol.21
, pp. 951-960
-
-
Söding, J.1
-
18
-
-
84864828679
-
GalaxyTBM: Template-based modeling by building a reliable core and refining unreliable local regions
-
Ko, J.; Park, H.; Seok, C. GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions BMC Bioinf. 2012, 13, 198 10.1186/1471-2105-13-198
-
(2012)
BMC Bioinf.
, vol.13
, pp. 198
-
-
Ko, J.1
Park, H.2
Seok, C.3
-
19
-
-
84904823376
-
GalaxySite: Ligand-binding site prediction by using molecular docking
-
Heo, L.; Shin, W.-H.; Lee, M. S.; Seok, C. GalaxySite: Ligand-binding site prediction by using molecular docking Nucleic Acids Res. 2014, 42, W210-W214 10.1093/nar/gku321
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. W210-W214
-
-
Heo, L.1
Shin, W.-H.2
Lee, M.S.3
Seok, C.4
-
20
-
-
84855642606
-
-
Tripos International, St. Louis, MO
-
SYBYL 8.1; Tripos International, St.: Louis, MO, 2008.
-
(2008)
SYBYL 8.1
-
-
-
21
-
-
84937469123
-
Effective protein model structure refinement by loop modeling and overall relaxation
-
Lee, G. R.; Heo, L.; Seok, C. Effective protein model structure refinement by loop modeling and overall relaxation Proteins: Struct., Funct., Genet. 2015, 10.1002/prot.24858
-
(2015)
Proteins: Struct., Funct., Genet.
-
-
Lee, G.R.1
Heo, L.2
Seok, C.3
-
22
-
-
84928550315
-
DOCK 6: Impact of New Features and Current Docking Performance
-
Allen, W. J.; Balius, T. E.; Mukherjee, S.; Brozell, S. R.; Moustakas, D. T.; Lang, P. T.; Case, D. A.; Kuntz, I. D.; Rizzo, R. C. DOCK 6: Impact of New Features and Current Docking Performance J. Comput. Chem. 2015, 36, 1132-1156 10.1002/jcc.23905
-
(2015)
J. Comput. Chem.
, vol.36
, pp. 1132-1156
-
-
Allen, W.J.1
Balius, T.E.2
Mukherjee, S.3
Brozell, S.R.4
Moustakas, D.T.5
Lang, P.T.6
Case, D.A.7
Kuntz, I.D.8
Rizzo, R.C.9
-
23
-
-
0036022960
-
Further Development and Validation of Empirical Scoring Functions for Structure-Based Binding Affinity Prediction
-
Wang, R.; Lai, L.; Wang, S. Further Development and Validation of Empirical Scoring Functions for Structure-Based Binding Affinity Prediction J. Comput.-Aided Mol. Des. 2002, 16, 11-26 10.1023/A:1016357811882
-
(2002)
J. Comput.-Aided Mol. Des.
, vol.16
, pp. 11-26
-
-
Wang, R.1
Lai, L.2
Wang, S.3
-
24
-
-
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 10.1006/jmbi.1999.3371
-
(2000)
J. Mol. Biol.
, vol.295
, pp. 337-356
-
-
Gohlke, H.1
Hendlich, M.2
Klebe, G.3
-
25
-
-
33846518797
-
In silico target fishing: Predicting biological targets from chemical structure
-
Jenkins, J. L.; Bender, A.; Davies, J. W. In silico target fishing: Predicting biological targets from chemical structure Drug Discovery Today: Technol. 2006, 3, 413-421 10.1016/j.ddtec.2006.12.008
-
(2006)
Drug Discovery Today: Technol.
, vol.3
, pp. 413-421
-
-
Jenkins, J.L.1
Bender, A.2
Davies, J.W.3
-
26
-
-
10344232638
-
Scoring Function for Automated Assessment of Protein Structure Template Quaility
-
Zhang, Y.; Skolnick, J. Scoring Function for Automated Assessment of Protein Structure Template Quaility Proteins: Struct., Funct., Genet. 2004, 57, 702-710 10.1002/prot.20264
-
(2004)
Proteins: Struct., Funct., Genet.
, vol.57
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
27
-
-
33748667774
-
Consensus scoring for protein-ligand interactions
-
Feher, M. Consensus scoring for protein-ligand interactions Drug Discovery Today 2006, 11, 421-428 10.1016/j.drudis.2006.03.009
-
(2006)
Drug Discovery Today
, vol.11
, pp. 421-428
-
-
Feher, M.1
-
28
-
-
67650077383
-
Influence of Protonation, Tautomeric, and Stereomeric States on Protein-Ligand Docking Results
-
ten Brink, T.; Exner, T. E. Influence of Protonation, Tautomeric, and Stereomeric States on Protein-Ligand Docking Results J. Chem. Inf. Model. 2009, 49, 1535-1546 10.1021/ci800420z
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1535-1546
-
-
Ten Brink, T.1
Exner, T.E.2
-
29
-
-
50249156843
-
Selective structure-based virtual screening for full and partial agonists of the beta2 adrengic receptor
-
de Graaf, C.; Rognan, D. Selective structure-based virtual screening for full and partial agonists of the beta2 adrengic receptor J. Med. Chem. 2008, 51, 4978-4985 10.1021/jm800710x
-
(2008)
J. Med. Chem.
, vol.51
, pp. 4978-4985
-
-
De Graaf, C.1
Rognan, D.2
-
30
-
-
79958181369
-
Implementation and Evaluation of a Docking-Rescoring Method using Molecular Footprint Comparisons
-
Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-Rescoring Method using Molecular Footprint Comparisons J. Comput. Chem. 2011, 32, 2273-2289 10.1002/jcc.21814
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 2273-2289
-
-
Balius, T.E.1
Mukherjee, S.2
Rizzo, R.C.3
|