-
1
-
-
42049088710
-
Statins increase p21 through inhibition of histone deacetylase activity and release of promoter-associated hdac1/2
-
Lin, Y.C., Lin, J.H., Chou, C.W., Chang, Y.F., Yeh, S.H. and Chen, C.C. (2008) Statins increase p21 through inhibition of histone deacetylase activity and release of promoter-associated HDAC1/2. Cancer Res., 68, 2375-2383.
-
(2008)
Cancer Res
, vol.68
, pp. 2375-2383
-
-
Lin, Y.C.1
Lin, J.H.2
Chou, C.W.3
Chang, Y.F.4
Yeh, S.H.5
Chen, C.C.6
-
2
-
-
11144323163
-
Virtual screening of chemical libraries
-
Shoichet, B.K. (2004) Virtual screening of chemical libraries. Nature, 432, 862-865.
-
(2004)
Nature
, vol.432
, pp. 862-865
-
-
Shoichet, B.K.1
-
3
-
-
0035342428
-
Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule
-
Chen, Y.Z. and Zhi, D.G. (2001) Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule. Proteins-Struct. Funct. Genet., 43, 217-226.
-
(2001)
Proteins-Struct. Funct. Genet.
, vol.43
, pp. 217-226
-
-
Chen, Y.Z.1
Zhi, D.G.2
-
4
-
-
70449634957
-
Predicting new molecular targets for known drugs
-
Keiser, M.J., Setola, V., Irwin, J.J., Laggner, C., Abbas, A.I., Hufeisen, S.J., Jensen, N.H., Kuijer, M.B., Matos, R.C., Tran, T.B. et al. (2009) Predicting new molecular targets for known drugs. Nature, 462, 175-U148.
-
(2009)
Nature
, vol.462
-
-
Keiser, M.J.1
Setola, V.2
Irwin, J.J.3
Laggner, C.4
Abbas, A.I.5
Hufeisen, S.J.6
Jensen, N.H.7
Kuijer, M.B.8
Matos, R.C.9
Tran, T.B.10
-
5
-
-
67849110009
-
Sepresa: A server for the prediction of populations susceptible to serious adverse drug reactions implementing the methodology of a chemical-protein interactome
-
Yang, L., Luo, H., Chen, J., Xing, Q.H. and He, L. (2009) SePreSA: a server for the prediction of populations susceptible to serious adverse drug reactions implementing the methodology of a chemical-protein interactome. Nucleic Acids Res., 37, W406-W412.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Yang, L.1
Luo, H.2
Chen, J.3
Xing, Q.H.4
He, L.5
-
6
-
-
70350512851
-
Target fishing for chemical compounds using target-ligand activity data and ranking based methods
-
Wale, N. and Karypis, G. (2009) Target fishing for chemical compounds using target-ligand activity data and ranking based methods. J. Chem. Inf. Model., 49, 2190-2201.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 2190-2201
-
-
Wale, N.1
Karypis, G.2
-
7
-
-
45749117025
-
Ranking targets in structure-based virtual screening of three-dimensional protein libraries: Methods and problems
-
Kellenberger, E., Foata, N. and Rognan, D. (2008) Ranking targets in structure-based virtual screening of three-dimensional protein libraries: methods and problems. J. Chem. Inf. Model., 48, 1014-1025.
-
(2008)
J. Chem. Inf. Model.
, vol.48
, pp. 1014-1025
-
-
Kellenberger, E.1
Foata, N.2
Rognan, D.3
-
8
-
-
79953100964
-
Structure-based systems biology for analyzing off-target binding
-
Xie, L. and Bourne, P.E. (2011) Structure-based systems biology for analyzing off-target binding. Curr. Opin. Struct. Biol., 21, 189-199.
-
(2011)
Curr. Opin. Struct. Biol.
, vol.21
, pp. 189-199
-
-
Xie, L.1
Bourne, P.E.2
-
9
-
-
80054928964
-
Robust scoring functions for protein-ligand interactions with quantum chemical charge models
-
Wang, J.C., Lin, J.H., Chen, C.M., Perryman, A.L. and Olson, A.J. (2011) Robust scoring functions for protein-ligand interactions with quantum chemical charge models. J. Chem. Inf. Model., 51, 2528-2537.
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 2528-2537
-
-
Wang, J.C.1
Lin, J.H.2
Chen, C.M.3
Perryman, A.L.4
Olson, A.J.5
-
10
-
-
33947716119
-
A semiempirical free energy force field with charge-based desolvation
-
Huey, R., Morris, G.M., Olson, A.J. and Goodsell, D.S. (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
Morris, G.M.2
Olson, A.J.3
Goodsell, D.S.4
-
11
-
-
3042524904
-
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges - The Resp model
-
Bayly, C.I., Cieplak, P., Cornell, W.D. and Kollman, P.A. (1993) A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges-the Resp model. J. Phys. Chem., 97, 10269-10280.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.D.3
Kollman, P.A.4
-
12
-
-
0001041959
-
Fast, efficient generation of high-quality atomic charges AM1-BCC model:I. Method
-
Jakalian, A., Bush, B.L., Jack, D.B. and Bayly, C.I. (2000) Fast, efficient generation of high-quality atomic Charges. AM1-BCC model: I. Method. J. Comput. Chem., 21, 132-146.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 132-146
-
-
Jakalian, A.1
Bush, B.L.2
Jack, D.B.3
Bayly, C.I.4
-
14
-
-
66149103553
-
Comparative assessment of scoring functions on a diverse test set
-
Cheng, T.J., Li, X., Li, Y., Liu, Z.H. and Wang, R.X. (2009) Comparative assessment of scoring functions on a diverse test set. J. Chem. Inf. Model., 49, 1079-1093.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1079-1093
-
-
Cheng, T.J.1
Li, X.2
Li, Y.3
Liu, Z.H.4
Wang, R.X.5
-
15
-
-
0037763817
-
Comparative evaluation of 11 scoring functions for molecular docking
-
Wang, R.X., Lu, Y.P. and Wang, S.M. (2003) Comparative evaluation of 11 scoring functions for molecular docking. J. Med. Chem, 46, 2287-2303.
-
(2003)
J. Med. Chem
, vol.46
, pp. 2287-2303
-
-
Wang, R.X.1
Lu, Y.P.2
Wang, S.M.3
-
16
-
-
23144462493
-
Medock: A web server for efficient prediction of ligand binding sites based on a novel optimization algorithm
-
Chang, D.T.H., Oyang, Y.J. and Lin, J.H. (2005) MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm. Nucleic Acids Res., 33, W233-W238.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Chang, D.T.H.1
Oyang, Y.J.2
Lin, J.H.3
-
17
-
-
77954321129
-
On the design of optimization algorithms for prediction of molecular interactions
-
Chang, D.T.H., Lin, J.H., Hsieh, C.H. and Oyang, Y.J. (2010) On the design of optimization algorithms for prediction of molecular interactions. Int. J. Artif. Intelligence Tools, 19, 267-280.
-
(2010)
Int. J. Artif. Intelligence Tools
, vol.19
, pp. 267-280
-
-
Chang, D.T.H.1
Lin, J.H.2
Hsieh, C.H.3
Oyang, Y.J.4
-
18
-
-
33748173818
-
BDT: An easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with autodock
-
Vaque, M., Arola, A., Aliagas, C. and Pujadas, G. (2006) BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock. Bioinformatics, 22, 1803-1804.
-
(2006)
Bioinformatics
, vol.22
, pp. 1803-1804
-
-
Vaque, M.1
Arola, A.2
Aliagas, C.3
Pujadas, G.4
-
19
-
-
33846155913
-
Structure-based maximal affinity model predicts small-molecule druggability
-
Cheng, A.C., Coleman, R.G., Smyth, K.T., Cao, Q., Soulard, P., Caffrey, D.R., Salzberg, A.C. and Huang, E.S. (2007) Structure-based maximal affinity model predicts small-molecule druggability. Nat. Biotechnol., 25, 71-75.
-
(2007)
Nat. Biotechnol.
, vol.25
, pp. 71-75
-
-
Cheng, A.C.1
Coleman, R.G.2
Smyth, K.T.3
Cao, Q.4
Soulard, P.5
Caffrey, D.R.6
Salzberg, A.C.7
Huang, E.S.8
-
20
-
-
33646228824
-
Sc-pdb: An annotated database of druggable binding sites from the protein data bank
-
Kellenberger, E., Muller, P., Schalon, C., Bret, G., Foata, N. and Rognan, D. (2006) sc-PDB: an annotated database of druggable binding sites from the protein data bank. J. Chem. Inf. Model., 46, 717-727.
-
(2006)
J. Chem. Inf. Model.
, vol.46
, pp. 717-727
-
-
Kellenberger, E.1
Muller, P.2
Schalon, C.3
Bret, G.4
Foata, N.5
Rognan, D.6
-
21
-
-
79954520873
-
Sc-pdb: A database for identifying variations and multiplicity of 'druggable' binding sites in proteins
-
Meslamani, J., Rognan, D. and Kellenberger, E. (2011) sc-PDB: a database for identifying variations and multiplicity of 'druggable' binding sites in proteins. Bioinformatics, 27, 1324-1326.
-
(2011)
Bioinformatics
, vol.27
, pp. 1324-1326
-
-
Meslamani, J.1
Rognan, D.2
Kellenberger, E.3
-
22
-
-
77949601825
-
CD-HIT Suite: A web server for clustering and comparing biological sequences
-
Huang, Y., Niu, B.F., Gao, Y., Fu, L.M. and Li, W.Z. (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics, 26, 680-682.
-
(2010)
Bioinformatics
, vol.26
, pp. 680-682
-
-
Huang, Y.1
Niu, B.F.2
Gao, Y.3
Fu, L.M.4
Li, W.Z.5
-
23
-
-
23144456254
-
Siteengines: Recognition and comparison of binding sites and protein-protein interfaces
-
Shulman-Peleg, A., Nussinov, R. and Wolfson, H.J. (2005) SiteEngines: recognition and comparison of binding sites and protein-protein interfaces. Nucleic Acids Res., 33, W337-W341.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Shulman-Peleg, A.1
Nussinov, R.2
Wolfson, H.J.3
-
24
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
Shindyalov, I.N. and Bourne, P.E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng., 11, 739-747.
-
(1998)
Protein Eng.
, vol.11
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
25
-
-
80053512597
-
Open Babel: An open chemical toolbox
-
O'Boyle, N.M., Banck, M., James, C.A., Morley, C., Vandermeersch, T. and Hutchison, G.R. (2011) Open Babel: an open chemical toolbox. J. Cheminform, 3, 33.
-
(2011)
J. Cheminform
, vol.3
, pp. 33
-
-
O'Boyle, N.M.1
Banck, M.2
James, C.A.3
Morley, C.4
Vandermeersch, T.5
Hutchison, G.R.6
-
26
-
-
20144382495
-
Discovery and selection of tmc114 a next generation HIV-1 protease inhibitor
-
Surleraux, D.L.N.G., Tahri, A., Verschueren, W.G., Pille, G.M.E., de Kock, H.A., Jonckers, T.H.M., Peeters, A., De Meyer, S., Azijn, H., Pauwels, R. et al. (2005) Discovery and selection of TMC114, a next generation HIV-1 protease inhibitor. J. Med. Chem, 48, 1813-1822.
-
(2005)
J. Med. Chem
, vol.48
, pp. 1813-1822
-
-
Surleraux, D.L.N.G.1
Tahri, A.2
Verschueren, W.G.3
Pille, G.M.E.4
De Kock, H.A.5
Jonckers, T.H.M.6
Peeters, A.7
De Meyer, S.8
Azijn, H.9
Pauwels, R.10
-
27
-
-
36048962439
-
Inverse in silico screening for identification of kinase inhibitor targets
-
Zahler, S., Tietze, S., Totzke, F., Kubbutat, M., Meijer, L., Vollmar, A.M. and Apostolakis, J. (2007) Inverse in silico screening for identification of kinase inhibitor targets. Chem. Biol., 14, 1207-1214.
-
(2007)
Chem. Biol.
, vol.14
, pp. 1207-1214
-
-
Zahler, S.1
Tietze, S.2
Totzke, F.3
Kubbutat, M.4
Meijer, L.5
Vollmar, A.M.6
Apostolakis, J.7
-
28
-
-
46649092697
-
Effect of flap mutations on structure of hiv-1 protease and inhibition by saquinavir and darunavir
-
Liu, F.L., Kovalevsky, A.Y., Tie, Y.F., Ghosh, A.K., Harrison, R.W. and Weber, I.T. (2008) Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir. J. Mol. Biol., 381, 102-115.
-
(2008)
J. Mol. Biol.
, vol.381
, pp. 102-115
-
-
Liu, F.L.1
Kovalevsky, A.Y.2
Tie, Y.F.3
Ghosh, A.K.4
Harrison, R.W.5
Weber, I.T.6
-
29
-
-
33144466093
-
Effectiveness of nonpeptide clinical inhibitor tmc-114 on hiv-1 protease with highly drug resistant mutations D30N, I50V, and L90M
-
Kovalevsky, A.Y., Tie, Y.F., Liu, F.L., Boross, P.I., Wang, Y.F., Leshchenko, S., Ghosh, A.K., Harrison, R.W. and Weber, I.T. (2006) Effectiveness of nonpeptide clinical inhibitor TMC-114 on HIV-1 protease with highly drug resistant mutations D30N, I50V, and L90M. J. Med. Chem, 49, 1379-1387.
-
(2006)
J. Med. Chem
, vol.49
, pp. 1379-1387
-
-
Kovalevsky, A.Y.1
Tie, Y.F.2
Liu, F.L.3
Boross, P.I.4
Wang, Y.F.5
Leshchenko, S.6
Ghosh, A.K.7
Harrison, R.W.8
Weber, I.T.9
-
30
-
-
11144354478
-
High resolution crystal structures of hiv-1 protease with a potent non-peptide inhibitor (UIC-94017) active against multi-drug-resistant clinical strains
-
Tie, Y.F., Boross, P.I., Wang, Y.F., Gaddis, L., Hussain, A.K., Leshchenko, S., Ghoshl, A.K., Louis, J.M., Harrison, R.W. and Weber, I.T. (2004) High resolution crystal structures of HIV-1 protease with a potent non-peptide inhibitor (UIC-94017) active against multi-drug-resistant clinical strains. J. Mol. Biol., 338, 341-352.
-
(2004)
J. Mol. Biol.
, vol.338
, pp. 341-352
-
-
Tie, Y.F.1
Boross, P.I.2
Wang, Y.F.3
Gaddis, L.4
Hussain, A.K.5
Leshchenko, S.6
Ghoshl, A.K.7
Louis, J.M.8
Harrison, R.W.9
Weber, I.T.10
-
31
-
-
2942544255
-
Binding of the potential antitumour agent indirubin-5-sulphonate at the inhibitor site of rabbit muscle glycogen phosphorylase b-Comparison with ligand binding to PCDK2-cyclin A complex
-
Kosmopoulou, M.N., Leonidas, D.D., Chrysina, E.D., Bischler, N., Eisenbrand, G., Sakarellos, C.E., Pauptit, R. and Oikonomakos, N.G. (2004) Binding of the potential antitumour agent indirubin-5-sulphonate at the inhibitor site of rabbit muscle glycogen phosphorylase b-comparison with ligand binding to pCDK2-cyclin A complex. Eur J. Biochem., 271, 2280-2290.
-
(2004)
Eur J. Biochem.
, vol.271
, pp. 2280-2290
-
-
Kosmopoulou, M.N.1
Leonidas, D.D.2
Chrysina, E.D.3
Bischler, N.4
Eisenbrand, G.5
Sakarellos, C.E.6
Pauptit, R.7
Oikonomakos, N.G.8
-
32
-
-
27544491192
-
ROCR: Visualizing classifier performance in R
-
Sing, T., Sander, O., Beerenwinkel, N. and Lengauer, T. (2005) ROCR: visualizing classifier performance in R. Bioinformatics, 21, 3940-3941.
-
(2005)
Bioinformatics
, vol.21
, pp. 3940-3941
-
-
Sing, T.1
Sander, O.2
Beerenwinkel, N.3
Lengauer, T.4
-
33
-
-
77952100365
-
Exploration of the hdac2 foot pocket: Synthesis and SAR of substituted N-(2-aminophenyl)benzamides
-
Bressi, J.C., Jennings, A.J., Skene, R., Wu, Y.Q., Melkus, R., De Jong, R., O'Connell, S., Grimshaw, C.E., Navre, M. and Gangloff, A.R. (2010) Exploration of the HDAC2 foot pocket: synthesis and SAR of substituted N-(2-aminophenyl)benzamides. Bioorg. Med. Chem. Lett, 20, 3142-3145.
-
(2010)
Bioorg. Med. Chem. Lett
, vol.20
, pp. 3142-3145
-
-
Bressi, J.C.1
Jennings, A.J.2
Skene, R.3
Wu, Y.Q.4
Melkus, R.5
De Jong, R.6
O'Connell, S.7
Grimshaw, C.E.8
Navre, M.9
Gangloff, A.R.10
-
34
-
-
84855879606
-
Interactions between buprenorphine and the protease inhibitors darunavir-ritonavir and fosamprenavir-ritonavir
-
Gruber, V.A., Rainey, P.M., Moody, D.E., Morse, G.D., Ma, Q., Prathikanti, S., Pade, P.A., Alvanzo, A.A.H. and McCance-Katz, E.F. (2012) Interactions between buprenorphine and the protease inhibitors darunavir-ritonavir and fosamprenavir-ritonavir. Clin. Infect. Dis., 54, 414-423.
-
(2012)
Clin. Infect. Dis.
, vol.54
, pp. 414-423
-
-
Gruber, V.A.1
Rainey, P.M.2
Moody, D.E.3
Morse, G.D.4
Ma, Q.5
Prathikanti, S.6
Pade, P.A.7
Alvanzo, A.A.H.8
McCance-Katz, E.F.9
-
35
-
-
66949122460
-
Drug interactions with new and investigational antiretrovirals
-
Brown, K.C., Paul, S. and Kashuba, A.D.M. (2009) Drug interactions with new and investigational antiretrovirals. Clin. Pharmacokinet., 48, 211-241.
-
(2009)
Clin. Pharmacokinet.
, vol.48
, pp. 211-241
-
-
Brown, K.C.1
Paul, S.2
Kashuba, A.D.M.3
-
36
-
-
0037364162
-
ADMET in silico modelling: Towards prediction paradise?
-
van de Waterbeemd, H. and Gifford, E. (2003) ADMET in silico modelling: towards prediction paradise? Nat. Rev. Drug Discov., 2, 192-204.
-
(2003)
Nat. Rev. Drug Discov.
, vol.2
, pp. 192-204
-
-
Van De Waterbeemd, H.1
Gifford, E.2
-
37
-
-
27444434892
-
Metasite: Understanding metabolism in human cytochromes from the perspective of the chemist
-
Cruciani, G., Carosati, E., De Boeck, B., Ethirajulu, K., Mackie, C., Howe, T. and Vianello, R. (2005) MetaSite: understanding metabolism in human cytochromes from the perspective of the chemist. J. Med. Chem, 48, 6970-6979.
-
(2005)
J. Med. Chem
, vol.48
, pp. 6970-6979
-
-
Cruciani, G.1
Carosati, E.2
De Boeck, B.3
Ethirajulu, K.4
MacKie, C.5
Howe, T.6
Vianello, R.7
-
38
-
-
63449139456
-
Structure of p-glycoprotein reveals a molecular basis for poly-specific drug binding
-
Aller, S.G., Yu, J., Ward, A., Weng, Y., Chittaboina, S., Zhuo, R.P., Harrell, P.M., Trinh, Y.T., Zhang, Q.H., Urbatsch, I.L. et al. (2009) Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding. Science, 323, 1718-1722
-
(2009)
Science
, vol.323
, pp. 1718-1722
-
-
Aller, S.G.1
Yu, J.2
Ward, A.3
Weng, Y.4
Chittaboina, S.5
Zhuo, R.P.6
Harrell, P.M.7
Trinh, Y.T.8
Zhang, Q.H.9
Urbatsch, I.L.10
|