-
1
-
-
0030111106
-
Molecular docking towards drug discovery
-
Gschwend, D. A.; Good, A. C.; Kuntz, I. D. Molecular docking towards drug discovery. J. Mol. Recognit. 1996, 9, 175-186.
-
(1996)
J. Mol. Recognit.
, vol.9
, pp. 175-186
-
-
Gschwend, D.A.1
Good, A.C.2
Kuntz, I.D.3
-
2
-
-
52649133007
-
Virtual screening of chemical libraries for drug discovery
-
Green, D. V. S. Virtual screening of chemical libraries for drug discovery. Expert Opin. Drug DiscoVery 2008, 3, 1011-1026.
-
(2008)
Expert Opin. Drug DiscoVery
, vol.3
, pp. 1011-1026
-
-
Green, D.V.S.1
-
3
-
-
39049094335
-
Virtual screening and its integration with modern drug design technologies
-
Guido, R. V. C.; Oliva, G.; Andricopulo, A. D. Virtual screening and its integration with modern drug design technologies. Curr. Med. Chem. 2008, 15, 37-46.
-
(2008)
Curr. Med. Chem.
, vol.15
, pp. 37-46
-
-
Guido, R.V.C.1
Oliva, G.2
Andricopulo, A.D.3
-
4
-
-
39449120398
-
Protein-ligand docking: A review of recent advances and future perspectives
-
DOI 10.2174/157341208783497597
-
(4) Vaque, M.; Ardrevol, A.; Blade, C.; Salvado, M. J.; Blay, M.; Fernandez-Larrea, J.; Arola, L.; Pujadas, G. Protein-ligand docking: A review of recent advances and future perspectives. Curr. Pharm. Anal. 2008, 4, 1-19. (Pubitemid 351266958)
-
(2008)
Current Pharmaceutical Analysis
, vol.4
, Issue.1
, pp. 1-19
-
-
Vaque, M.1
Ardevol, A.2
Blade, C.3
Salvado, M.J.4
Blay, M.5
Fernandez-Larrea, J.6
Arola, L.7
Pujadas, G.8
-
5
-
-
0001679526
-
Assessing search strategies for flexible docking
-
(5) Vieth, M.; Hirst, J. D.; Dominy, B. N.; Daigler, H.; Brooks, C. L. Assessing search strategies for flexible docking. J. Comput. Chem. 1998, 19, 1623-1631. (Pubitemid 128590221)
-
(1998)
Journal of Computational Chemistry
, vol.19
, Issue.14
, pp. 1623-1631
-
-
Vieth, M.1
Hirst, J.D.2
Dominy, B.N.3
Daigler, H.4
Brooks III, C.L.5
-
6
-
-
0000231302
-
Assessing energy functions for flexible docking
-
(6) Vieth, M.; Hirst, J. D.; Kolinski, A.; Brooks, C. L. Assessing energy functions for flexible docking. J. Comput. Chem. 1998, 19, 1612-1622. (Pubitemid 128590220)
-
(1998)
Journal of Computational Chemistry
, vol.19
, Issue.14
, pp. 1612-1622
-
-
Vieth, M.1
Hirst, J.D.2
Kolinski, A.3
Brooks III, C.L.4
-
8
-
-
0036520840
-
A review of proteinsmall molecule docking methods
-
Taylor, R. D.; Jewsbury, P. J.; Essex, J. W. A review of proteinsmall molecule docking methods. J. Comput.-Aided Mol. Des. 2002, 16, 151-166.
-
(2002)
J. Comput.-Aided Mol. Des.
, vol.16
, pp. 151-166
-
-
Taylor, R.D.1
Jewsbury, P.J.2
Essex, J.W.3
-
9
-
-
33749513370
-
Scoring functions for protein-ligand docking
-
Jain, A. N. Scoring functions for protein-ligand docking. Curr. Protein Pept. Sci. 2006, 7, 407-420.
-
(2006)
Curr. Protein Pept. Sci.
, vol.7
, pp. 407-420
-
-
Jain, A.N.1
-
10
-
-
33750124980
-
Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes
-
Friesner, R. A.; Murphy, R. B.; Repasky, M. P.; Frye, L. L.; Greenwood, J. R.; Halgren, T. A.; Sanschagrin, P. C.; Mainz, D. T. Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J. Med. Chem. 2006, 49, 6177-6196.
-
(2006)
J. Med. Chem.
, vol.49
, pp. 6177-6196
-
-
Friesner, R.A.1
Murphy, R.B.2
Repasky, M.P.3
Frye, L.L.4
Greenwood, J.R.5
Halgren, T.A.6
Sanschagrin, P.C.7
Mainz, D.T.8
-
11
-
-
0942276314
-
A quantum mechanics-based scoring function: Study of zinc ion-mediated ligand binding
-
Raha, K.; Merz, K. M. A quantum mechanics-based scoring function: Study of zinc ion-mediated ligand binding. J. Am. Chem. Soc. 2004, 126, 1020-1021.
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 1020-1021
-
-
Raha, K.1
Merz, K.M.2
-
12
-
-
20344403522
-
Importance of accurate charges in molecular docking: Quantum Mechanical/Molecular Mechanical (QM/MM) approach
-
DOI 10.1002/jcc.20222
-
(12) Cho, A. E.; Guallar, V.; Berne, B. J.; Friesner, R. Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach. J. Comput. Chem. 2005, 26, 915-931. (Pubitemid 40860395)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.9
, pp. 915-931
-
-
Cho, A.E.1
Guallar, V.2
Berne, B.J.3
Friesner, R.4
-
13
-
-
56649118415
-
Effect of quantum mechanical charges in binding sites of metalloproteins
-
Cho, A. E. Effect of Quantum Mechanical Charges in Binding Sites of Metalloproteins. BioChip J. 2007, 1, 70-75.
-
(2007)
BioChip J.
, vol.1
, pp. 70-75
-
-
Cho, A.E.1
-
14
-
-
70449091473
-
Quantum mechanical calculations for binding sites of metalloproteins
-
Cho, A. E. Quantum Mechanical Calculations for Binding Sites of Metalloproteins. BioChip J. 2008, 2, 148-153.
-
(2008)
BioChip J.
, vol.2
, pp. 148-153
-
-
Cho, A.E.1
-
15
-
-
70349934530
-
Extension of QM/MM docking and its applications to metalloproteins
-
DOI: 10.1002/jcc.21270.
-
Cho, A. E.; Rinaldo, D. Extension of QM/MM Docking and its Applications to Metalloproteins. J. Comput. Chem. DOI: 10.1002/jcc.21270.
-
J. Comput. Chem.
-
-
Cho, A.E.1
Rinaldo, D.2
-
16
-
-
2542530042
-
The PDBbind database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures
-
DOI 10.1021/jm030580l
-
(16) Wang, R.; Fang, X.; Lu, Y.; Wang, S. The PDBbind Database: Collection of Binding Affinities for Protein-Ligand Complexes with Known Three-Dimensional Structures. J. Med. Chem. 2004, 47, 2977-2980. (Pubitemid 38702694)
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.12
, pp. 2977-2980
-
-
Wang, R.1
Fang, X.2
Lu, Y.3
Wang, S.4
-
17
-
-
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.
-
(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
-
18
-
-
37749011993
-
Epik: A software program for pK (a) prediction and protonation state generation for drug-like molecules
-
Shelley, J. C.; Cholleti, A.; Frye, L. L.; Greenwood, J. R.; Timlin, M. R.; Uchimaya, M. Epik: a software program for pK (a) prediction and protonation state generation for drug-like molecules. J. Comput.-Aided Mol. Des. 2007, 21, 681-691.
-
(2007)
J. Comput.-Aided Mol. Des.
, vol.21
, pp. 681-691
-
-
Shelley, J.C.1
Cholleti, A.2
Frye, L.L.3
Greenwood, J.R.4
Timlin, M.R.5
Uchimaya, M.6
-
19
-
-
65249117514
-
Identifying and characterizing binding sites and assessing druggability
-
Halgren, T. A. Identifying and Characterizing Binding Sites and Assessing Druggability. J. Chem. Inf. Model 2009, 49, 377-389.
-
(2009)
J. Chem. Inf. Model
, vol.49
, pp. 377-389
-
-
Halgren, T.A.1
-
20
-
-
12144289984
-
Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
-
Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. 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
Shaw, D.E.11
Francis, P.12
Shenkin, P.S.13
-
21
-
-
0031226772
-
Empirical scoring functions 0.1. the development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
-
Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. Empirical scoring functions 0.1. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J. Comput.-Aided Mol. Des. 1997, 11, 425-445.
-
(1997)
J. Comput.-Aided Mol. Des.
, vol.11
, pp. 425-445
-
-
Eldridge, M.D.1
Murray, C.W.2
Auton, T.R.3
Paolini, G.V.4
Mee, R.P.5
-
22
-
-
70350467525
-
-
Schrödinger, LLC: Portland, OR
-
QM-Polarized Ligand Docking; Schrödinger, LLC: Portland, OR, 2006.
-
(2006)
QM-Polarized Ligand Docking
-
-
-
23
-
-
70350469833
-
-
Version 3.5; Schrodinger, LLC: Portland, OR
-
QSite, Version 3.5; Schrodinger, LLC: Portland, OR, 2004.
-
(2004)
QSite
-
-
-
24
-
-
3042806401
-
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
-
Perola, E.; Walters, W. P.; Charifson, P. S. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins: Struct., Funct., Bioinf. 2004, 56, 235-249.
-
(2004)
Proteins: Struct., Funct., Bioinf.
, vol.56
, pp. 235-249
-
-
Perola, E.1
Walters, W.P.2
Charifson, P.S.3
-
25
-
-
60349119258
-
Form follows function: Shape analysis of protein cavities for receptor-based drug design
-
Weisel, M.; Proschak, E.; Kriegl, J. M.; Schneider, G. Form follows function: Shape analysis of protein cavities for receptor-based drug design. Proteomics 2009, 9, 451-459.
-
(2009)
Proteomics
, vol.9
, pp. 451-459
-
-
Weisel, M.1
Proschak, E.2
Kriegl, J.M.3
Schneider, G.4
-
26
-
-
38049162232
-
Quantitative analysis on the characteristics of targets with FDA approved drugs
-
Sakharkar, M. K.; Li, P.; Zhong, Z. W.; Sakharkar, K. R. Quantitative analysis on the characteristics of targets with FDA approved drugs. Int. J. Biol. Sci. 2008, 4, 15-22.
-
(2008)
Int. J. Biol. Sci.
, vol.4
, pp. 15-22
-
-
Sakharkar, M.K.1
Li, P.2
Zhong, Z.W.3
Sakharkar, K.R.4
-
27
-
-
34447648367
-
Fragment-based drug design: Combining philosophy with technology. Curr. Opin. Drug Discovery
-
Bartoli, S.; Fincham, C. I.; Fattori, D. Fragment-based drug design: Combining philosophy with technology. Curr. Opin. Drug Discovery DeV. 2007, 10, 422-429.
-
(2007)
DeV.
, vol.10
, pp. 422-429
-
-
Bartoli, S.1
Fincham, C.I.2
Fattori, D.3
-
28
-
-
33846524439
-
Motifs for molecular recognition exploiting hydrophobic enclosure in proteinligand binding
-
Young, T.; Abel, R.; Kim, B.; Berne, B. J.; Friesner, R. A. Motifs for molecular recognition exploiting hydrophobic enclosure in proteinligand binding. Proc. Natl. Acad. Sci. 2007, 104, 808-813.
-
(2007)
Proc. Natl. Acad. Sci.
, vol.104
, pp. 808-813
-
-
Young, T.1
Abel, R.2
Kim, B.3
Berne, B.J.4
Friesner, R.A.5
|