-
2
-
-
34250827919
-
Analysis of HIV wild-type and mutant structures via in silico docking against diverse ligand libraries
-
Chang, M. et al. (2007)Analysis of HIV wild-type and mutant structures via in silico docking against diverse ligand libraries. J. Chem. Inf. Model., 47, 1258-1262.
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 1258-1262
-
-
Chang, M.1
-
3
-
-
47149102700
-
Empirical entropic contributions in computational docking: evaluation in APS reductase complexes
-
Chang, M. et al. (2008)Empirical entropic contributions in computational docking: evaluation in APS reductase complexes. J. Comput. Chem., 29, 1753-1761.
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 1753-1761
-
-
Chang, M.1
-
4
-
-
0346962971
-
Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions
-
Deng, Z. et al. (2004) Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. J. Med. Chem., 47, 337-344.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 337-344
-
-
Deng, Z.1
-
5
-
-
58149141782
-
Structure of the complex between phosphorylated substrates and the SCF β-TrCP ubiquitin ligase receptor: a combined NMR, molecular modeling, and docking approach
-
Evrard-Todeschi, N. et al. (2008) Structure of the complex between phosphorylated substrates and the SCF β-TrCP ubiquitin ligase receptor: a combined NMR, molecular modeling, and docking approach. J. Chem. Inf. Model., 48, 2350-2361.
-
(2008)
J. Chem. Inf. Model.
, vol.48
, pp. 2350-2361
-
-
Evrard-Todeschi, N.1
-
6
-
-
0344033635
-
PDB file parser and structure class implemented in Python
-
Hamelryck, T. and Manderick, B. (2003)PDB file parser and structure class implemented in Python. Bioinformatics, 19, 2308-2310.
-
(2003)
Bioinformatics
, vol.19
, pp. 2308-2310
-
-
Hamelryck, T.1
Manderick, B.2
-
7
-
-
33947716119
-
A semiempirical free energy force field with charge-based desolvation
-
Huey, R. et al. (2007) A semiempirical free energy force field with charge-based desolvation. J. Comput. Chem., 28, 1145-1152.
-
(2007)
J. Comput. Chem.
, vol.28
, pp. 1145-1152
-
-
Huey, R.1
-
8
-
-
0037434582
-
Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine
-
Jain, A. (2003) Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. J. Med. Chem., 46, 499-511.
-
(2003)
J. Med. Chem.
, vol.46
, pp. 499-511
-
-
Jain, A.1
-
9
-
-
33644792666
-
Update of the drug resistance mutations in HIV-1: fall 2005
-
Johnson, V. et al. (2005) Update of the drug resistance mutations in HIV-1: fall 2005. Top HIV Med., 13, 125-131.
-
(2005)
Top HIV Med.
, vol.13
, pp. 125-131
-
-
Johnson, V.1
-
10
-
-
8844263008
-
Docking and scoring in virtual screening for drug discovery: methods and applications
-
Kitchen, D.B. et al. (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat. Rev. Drug Discov., 3, 935-949.
-
(2004)
Nat. Rev. Drug Discov.
, vol.3
, pp. 935-949
-
-
Kitchen, D.B.1
-
11
-
-
0003410791
-
-
Springer Series in Information Sciences, Heidelberg, Germany
-
Kohonen, T. (2001) Self-Organizing Maps. Springer Series in Information Sciences, Heidelberg, Germany.
-
(2001)
Self-Organizing Maps
-
-
Kohonen, T.1
-
12
-
-
33846108633
-
Binding DB: a web-accessible database of experimentally determined protein-ligand binding affinities
-
Liu, T. et al. (2007)BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res., 35, D198-D201.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Liu, T.1
-
13
-
-
0030572617
-
A comparison of SOM neural network and hierarchical clustering methods
-
Mangiameli, P. et al. (1996) A comparison of SOM neural network and hierarchical clustering methods. Eur. J. Oper. Res., 93, 402-417.
-
(1996)
Eur. J. Oper. Res.
, vol.93
, pp. 402-417
-
-
Mangiameli, P.1
-
14
-
-
11644261806
-
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
-
Morris, G. et al. (1998)Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem., 19, 1639-1662.
-
(1998)
J. Comput. Chem.
, vol.19
, pp. 1639-1662
-
-
Morris, G.1
-
15
-
-
50149103756
-
Synergies of virtual screening approaches
-
Muegge, I. (2008) Synergies of virtual screening approaches. Mini Rev. Med. Chem., 8, 927-933.
-
(2008)
Mini Rev. Med. Chem.
, vol.8
, pp. 927-933
-
-
Muegge, I.1
-
16
-
-
41549114720
-
Maximum common binding modes (MCBM): consensus docking scoring using multiple ligand information and interaction fingerprints
-
Renner, S. et al. (2008) Maximum common binding modes (MCBM): consensus docking scoring using multiple ligand information and interaction fingerprints. J. Chem. Inf. Model., 48, 319-332.
-
(2008)
J. Chem. Inf. Model.
, vol.48
, pp. 319-332
-
-
Renner, S.1
-
17
-
-
33746620870
-
TreeSOM: cluster analysis in the self-organizing map
-
Samsonova, E.V. et al. (2006) TreeSOM: cluster analysis in the self-organizing map. Neural Netw., 19, 935-949.
-
(2006)
Neural Netw.
, vol.19
, pp. 935-949
-
-
Samsonova, E.V.1
-
18
-
-
0035896038
-
Docking ligands onto binding site representations derived from proteins built by homology modelling
-
Schafferhans, A. and Klebe, G. (2001) Docking ligands onto binding site representations derived from proteins built by homology modelling. J. Mol. Biol., 307, 407-427.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 407-427
-
-
Schafferhans, A.1
Klebe, G.2
-
19
-
-
7544226311
-
PRODRG: a tool for high-throughput crystallography of protein-ligand complexes
-
Schüttelkopf, A. and van Aalten, D. (2004) PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Cryst., 60, 1355-1363.
-
(2004)
Acta Cryst.
, vol.60
, pp. 1355-1363
-
-
Schüttelkopf, A.1
van Aalten, D.2
-
20
-
-
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. et al. (2005)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., 48, 2534-2547.
-
(2005)
J. Med. Chem.
, vol.48
, pp. 2534-2547
-
-
Triballeau, N.1
-
21
-
-
17144414125
-
Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MMPB/SA
-
Wang, J. et al. (2005)Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MMPB/SA. J. Med. Chem., 48, 2432-2444.
-
(2005)
J. Med. Chem.
, vol.48
, pp. 2432-2444
-
-
Wang, J.1
-
22
-
-
0035910029
-
Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance
-
Wang, W. and Kollman, P. (2001)Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance. Proc. Natl Acad. Sci. USA, 98, 14937-14942.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 14937-14942
-
-
Wang, W.1
Kollman, P.2
-
23
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
Warren, G.L. et al. (2006) A critical assessment of docking programs and scoring functions. J. Med. Chem., 49, 5912-5931.
-
(2006)
J. Med. Chem.
, vol.49
, pp. 5912-5931
-
-
Warren, G.L.1
-
24
-
-
40649094486
-
Towards improving compound selection in structure-based virtual screening
-
Waszkowycz, B. (2008) Towards improving compound selection in structure-based virtual screening. Drug Discov. Today, 13, 219-226.
-
(2008)
Drug Discov. Today
, vol.13
, pp. 219-226
-
-
Waszkowycz, B.1
-
25
-
-
23844555629
-
Consensus scoring criteria for improving enrichment in virtual screening
-
Yang, J. et al. (2005)Consensus scoring criteria for improving enrichment in virtual screening. J. Chem. Inf. Model., 45, 1134-1146.
-
(2005)
J. Chem. Inf. Model.
, vol.45
, pp. 1134-1146
-
-
Yang, J.1
|