-
1
-
-
0033954256
-
The protein data bank
-
Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235-42.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
2
-
-
0036406643
-
A new method to detect related function among proteins independent of sequence and fold homology
-
Schmitt, S.; Kuhn, D.; Klebe, G. A new method to detect related function among proteins independent of sequence and fold homology. J. Mol. Biol. 2000, 323, 387-406.
-
(2000)
J. Mol. Biol.
, vol.323
, pp. 387-406
-
-
Schmitt, S.1
Kuhn, D.2
Klebe, G.3
-
3
-
-
0037661398
-
A new bioinformatic approach to detect common 3D sites in protein structures
-
Jambon, M.; Imberty, A.; Deleage, G.; Geourjon, C A new bioinformatic approach to detect common 3D sites in protein structures. Proteins 2003, 52, 137-145.
-
(2003)
Proteins
, vol.52
, pp. 137-145
-
-
Jambon, M.1
Imberty, A.2
Deleage, G.3
Geourjon, C.4
-
4
-
-
2442614144
-
Recognition of functional sites in protein structures
-
Shulman-Peleg, A.; Nussinov, R.; Wolfson, H. J. Recognition of functional sites in protein structures. J. Mol. Biol. 2004, 339, 607-633.
-
(2004)
J. Mol. Biol.
, vol.339
, pp. 607-633
-
-
Shulman-Peleg, A.1
Nussinov, R.2
Wolfson, H.J.3
-
5
-
-
33644876699
-
SitesBase: A database for structure-based protein-ligand binding site comparisons
-
Gold, N. D.; Jackson, R. M. SitesBase: A database for structure-based protein-ligand binding site comparisons. Nucleic Acids Res. 2006, 34, D231-234.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Gold, N.D.1
Jackson, R.M.2
-
6
-
-
33748449489
-
STRUCTFAST: Protein sequence remote homology detection and alignment using novel dynamic programming and profile-profile scoring
-
Debe, D. A.; Danzer, J. F.; Goddard, W. A.; Poleksic, A. STRUCTFAST: Protein sequence remote homology detection and alignment using novel dynamic programming and profile-profile scoring. Proteins 2006, 64 (4), 960-7.
-
(2006)
Proteins
, vol.64
, Issue.4
, pp. 960-967
-
-
Debe, D.A.1
Danzer, J.F.2
Goddard, W.A.3
Poleksic, A.4
-
7
-
-
34548778124
-
A novel approach to local similarity of protein binding sites substantially improves computational drug design results
-
Ramensky, V.; Sobol, A.; Zaitseva, N.; Rubinov, A.; Zosimov, V. A novel approach to local similarity of protein binding sites substantially improves computational drug design results. Proteins 2007, 69, 349-57.
-
(2007)
Proteins
, vol.69
, pp. 349-357
-
-
Ramensky, V.1
Sobol, A.2
Zaitseva, N.3
Rubinov, A.4
Zosimov, V.5
-
8
-
-
44349119204
-
A simple and fuzzy method to align and compare druggable ligand-binding sites
-
Jun
-
Schalon, C.; Surgand, J.-S.; Kellenberger, E.; Rognan, D. A simple and fuzzy method to align and compare druggable ligand-binding sites. Proteins 2008Jun, 71 (4), 1755-78.
-
(2008)
Proteins
, vol.71
, Issue.4
, pp. 1755-1778
-
-
Schalon, C.1
Surgand, J.-S.2
Kellenberger, E.3
Rognan, D.4
-
9
-
-
61449104961
-
Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques
-
Brenke, R.; Kozakov, D.; Chuang, G. Y.; Beglov, D.; Hall, D.; Landon, M. R.; Mattos, C.; Vajda, S. Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics 2009, 25 (5), 621-7.
-
(2009)
Bioinformatics
, vol.25
, Issue.5
, pp. 621-627
-
-
Brenke, R.1
Kozakov, D.2
Chuang, G.Y.3
Beglov, D.4
Hall, D.5
Landon, M.R.6
Mattos, C.7
Vajda, S.8
-
10
-
-
77956040809
-
Pocket similarity: Are alpha carbons enough?
-
Feldman, H. J.; Labute, P. Pocket similarity: are alpha carbons enough? J. Chem. Inf. Model. 2010, 50 (8), 1466-75.
-
(2010)
J. Chem. Inf. Model.
, vol.50
, Issue.8
, pp. 1466-1475
-
-
Feldman, H.J.1
Labute, P.2
-
11
-
-
65249163786
-
Functional annotation strategy for protein structures
-
Doppelt, O.; Moriaud, F.; Bornot, A.; de Brevern, A. G. Functional annotation strategy for protein structures. Bioinformation 2007, 1 (9), 357-9.
-
(2007)
Bioinformation
, vol.1
, Issue.9
, pp. 357-359
-
-
Doppelt, O.1
Moriaud, F.2
Bornot, A.3
De Brevern, A.G.4
-
12
-
-
67650670907
-
A review of MED-SuMo applications
-
Doppelt-Azeroual, O.; Moriaud, F.; Adcock, S. A.; Delfaud, F. A review of MED-SuMo applications. Infect. Disord.: Drug Targets 2009, 9 (3), 344-57, review.
-
(2009)
Infect. Disord.: Drug Targets
, vol.9
, Issue.3
, pp. 344-357
-
-
Doppelt-Azeroual, O.1
Moriaud, F.2
Adcock, S.A.3
Delfaud, F.4
-
13
-
-
77950284284
-
Fast and automated functional classification with MED-SuMo: An application on purine-binding proteins
-
Doppelt-Azeroual, O.; Delfaud, F.; Moriaud, F.; de Brevern, A. G. Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins. Protein Sci. 2010, 19 (4), 847-67.
-
(2010)
Protein Sci.
, vol.19
, Issue.4
, pp. 847-867
-
-
Doppelt-Azeroual, O.1
Delfaud, F.2
Moriaud, F.3
De Brevern, A.G.4
-
14
-
-
79960779897
-
Identify drug repurposing candidates by mining the protein data bank
-
doi: 10.1093/bib/bbr017, accessed online April 21, 2011
-
Moriaud F.; Richard S. B.; Adcock S. A.; Chanas-Martin L.; Surgand J.-S.; Ben Jelloul M.; Delfaud F. Identify drug repurposing candidates by mining the Protein Data Bank. In Briefings Bioinf. 2011, doi: 10.1093/bib/bbr017, accessed online April 21, 2011.
-
(2011)
Briefings Bioinf.
-
-
Moriaud, F.1
Richard, S.B.2
Adcock, S.A.3
Chanas-Martin, L.4
Surgand, J.-S.5
Ben Jelloul, M.6
Delfaud, F.7
-
15
-
-
65249116422
-
Computational fragment-based approach at PDB scale by protein local similarity
-
Feb
-
Moriaud, F.; Doppelt-Azeroual, O.; Martin, L.; Oguievetskaia, K.; Koch, K.; Vorotyntsev, A.; Adcock, S. A.; Delfaud, F. Computational fragment-based approach at PDB scale by protein local similarity. J. Chem. Inf. Model. 2009Feb, 49 (2), 280-94.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, Issue.2
, pp. 280-294
-
-
Moriaud, F.1
Doppelt-Azeroual, O.2
Martin, L.3
Oguievetskaia, K.4
Koch, K.5
Vorotyntsev, A.6
Adcock, S.A.7
Delfaud, F.8
-
16
-
-
67650986123
-
Computational fragment-based drug design to explore the hydrophobic sub pocket of the mitotic kinesin Eg5 allosteric binding site
-
Oguievetskaia, K.; Martin-Chanas, L.; Vorotyntsev, A.; Doppelt- Azeroual, O.; Brotel, X.; Adcock, S. A.; de Brevern, A. G.; Delfaud, F.; Moriaud, F. Computational fragment-based drug design to explore the hydrophobic sub pocket of the mitotic kinesin Eg5 allosteric binding site. J. Comput.-Aided Mol. Des. 2009, 23 (8), 571-82.
-
(2009)
J. Comput.-Aided Mol. Des.
, vol.23
, Issue.8
, pp. 571-582
-
-
Oguievetskaia, K.1
Martin-Chanas, L.2
Vorotyntsev, A.3
Doppelt- Azeroual, O.4
Brotel, X.5
Adcock, S.A.6
De Brevern, A.G.7
Delfaud, F.8
Moriaud, F.9
-
17
-
-
2442647742
-
BREED: Generating novel inhibitors through hybridization of known ligands. Application to CDK2, p38, and HIV protease
-
Pierce, A. C.; Rao, G.; Bemis, G. W. BREED: Generating novel inhibitors through hybridization of known ligands. Application to CDK2, p38, and HIV protease. J. Med. Chem. 2004, 47, 2768-75.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 2768-2775
-
-
Pierce, A.C.1
Rao, G.2
Bemis, G.W.3
-
18
-
-
33750836761
-
Identification of targetspecific bioisosteric fragments from ligand-protein crystallographic data
-
Kennewell, E. A.; Willett, P.; Ducrot, P.; Luttmann, C. Identification of targetspecific bioisosteric fragments from ligand-protein crystallographic data. J. Comput.-Aided Mol. Des. 2006, 20 (6), 385-94.
-
(2006)
J. Comput.-Aided Mol. Des.
, vol.20
, Issue.6
, pp. 385-394
-
-
Kennewell, E.A.1
Willett, P.2
Ducrot, P.3
Luttmann, C.4
-
19
-
-
77952732009
-
Bioisosteric replacement and scaffold hopping in lead generation and optimization
-
Langdon, S. R.; Ertl, P.; Brown, N. Bioisosteric replacement and scaffold hopping in lead generation and optimization. Mol. Inf. 2010, 29 (5).
-
(2010)
Mol. Inf.
, vol.29
, Issue.5
-
-
Langdon, S.R.1
Ertl, P.2
Brown, N.3
-
20
-
-
79955419410
-
Synopsis of some recent tactical application of bioisosteres in drug design
-
Meanwell, N. A. Synopsis of some recent tactical application of bioisosteres in drug design. J. Med. Chem. 2011, 54 (8), 2529-91.
-
(2011)
J. Med. Chem.
, vol.54
, Issue.8
, pp. 2529-2591
-
-
Meanwell, N.A.1
-
21
-
-
4544344217
-
Ligand Depot: A data warehouse for ligands bound to macromolecules
-
Feng, Z.; Chen, L.; Maddula, H.; Akcan, O.; Oughtred, R.; Berman, H. M.; Westbrook, J. Ligand Depot: A data warehouse for ligands bound to macromolecules. Bioinformatics 2004, 20 (13), 2153-5.
-
(2004)
Bioinformatics
, vol.20
, Issue.13
, pp. 2153-2155
-
-
Feng, Z.1
Chen, L.2
Maddula, H.3
Akcan, O.4
Oughtred, R.5
Berman, H.M.6
Westbrook, J.7
-
22
-
-
0002404088
-
On the orthogonal transformation used for structural comparisons
-
Kearsley, S. K. On the orthogonal transformation used for structural comparisons. Acta Crystallogr., Sect. A 1989, 45, 208-210.
-
(1989)
Acta Crystallogr., Sect. A
, vol.45
, pp. 208-210
-
-
Kearsley, S.K.1
-
23
-
-
60549090996
-
Synthesis of alkenyldiarylmethanes (ADAMs) containing benzo[d]isoxazole and oxazolidin-2-one rings, a new series of potent non-nucleoside HIV-1 reverse transcriptase inhibitors
-
Mar
-
Deng, B. L.; Zhao, Y.; Hartman, T. L.; Watson, K.; Buckheit, R. W., Jr.; Pannecouque, C.; De Clercq, E.; Cushman, M. Synthesis of alkenyldiarylmethanes (ADAMs) containing benzo[d]isoxazole and oxazolidin-2-one rings, a new series of potent non-nucleoside HIV-1 reverse transcriptase inhibitors. Eur. J. Med. Chem. 2009Mar, 44 (3), 1210-4.
-
(2009)
Eur. J. Med. Chem.
, vol.44
, Issue.3
, pp. 1210-1214
-
-
Deng, B.L.1
Zhao, Y.2
Hartman, T.L.3
Watson, K.4
Buckheit Jr., R.W.5
Pannecouque, C.6
De Clercq, E.7
Cushman, M.8
-
24
-
-
33846108633
-
BindingDB: A web-accessible database of experimentally determined protein-ligand binding affinities
-
Liu, T.; Lin, Y.; Wen, X.; Jorrisen, R. N.; Gilson, M. K. BindingDB: A web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res. 2007, 35, D198-D201.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Liu, T.1
Lin, Y.2
Wen, X.3
Jorrisen, R.N.4
Gilson, M.K.5
-
25
-
-
67349154388
-
Different poses for ligand and chaperone in inhibitor-bound Hsp90 and GRP94: Implications for paralog-specific drug design
-
Immormino, R. M.; Metzger, L. E.; Reardon, P. N.; Dollins, D. E.; Blagg, B. S.; Gewirth, D. T. Different poses for ligand and chaperone in inhibitor-bound Hsp90 and GRP94: Implications for paralog-specific drug design. J. Mol. Biol. 2009, 388, 1033-1042.
-
(2009)
J. Mol. Biol.
, vol.388
, pp. 1033-1042
-
-
Immormino, R.M.1
Metzger, L.E.2
Reardon, P.N.3
Dollins, D.E.4
Blagg, B.S.5
Gewirth, D.T.6
-
26
-
-
0033985080
-
GHKL, an emergent ATPase/kinase superfamily
-
Dutta, R.; Inouye, M. GHKL, an emergent ATPase/kinase superfamily. Trends Biochem. Sci. 2000, 25 (1), 24-28.
-
(2000)
Trends Biochem. Sci.
, vol.25
, Issue.1
, pp. 24-28
-
-
Dutta, R.1
Inouye, M.2
-
27
-
-
39149136212
-
Discovery of benzisoxazoles as potent inhibitors of chaperone heat shock protein 90
-
Gopalsamy, A.; Shi, M.; Golas, J.; Vogan, E.; Jacob, J.; Johnson, M.; Lee, F.; Nilakantan, R.; Petersen, R.; Svenson, K.; Chopra, R.; Tam, M. S.; Wen, Y.; Ellingboe, J.; Arndt, K.; Boschelli, F. Discovery of benzisoxazoles as potent inhibitors of chaperone heat shock protein 90. J. Med. Chem. 2008, 51, 373-375.
-
(2008)
J. Med. Chem.
, vol.51
, pp. 373-375
-
-
Gopalsamy, A.1
Shi, M.2
Golas, J.3
Vogan, E.4
Jacob, J.5
Johnson, M.6
Lee, F.7
Nilakantan, R.8
Petersen, R.9
Svenson, K.10
Chopra, R.11
Tam, M.S.12
Wen, Y.13
Ellingboe, J.14
Arndt, K.15
Boschelli, F.16
-
28
-
-
84905561271
-
-
The PubChem Project. http://pubchem.ncbi.nlm.nih.gov.
-
-
-
-
29
-
-
34548489855
-
Discovery of novel benzimidazoles as potent inhibitors of TIE-2 and VEGFR-2 tyrosine kinase receptors
-
Hasegawa, M.; Nishigaki, N.; Washio, Y.; Kano, K.; Harris, P. A.; Sato, H.; Mori, I.; West, R. I.; Shibahara, M.; Toyoda, H.; Wang, L.; Nolte, R. T.; Veal, J. M.; Cheung, M. Discovery of novel benzimidazoles as potent inhibitors of TIE-2 and VEGFR-2 tyrosine kinase receptors. J. Med. Chem. 2007, 50, 4453-4470.
-
(2007)
J. Med. Chem.
, vol.50
, pp. 4453-4470
-
-
Hasegawa, M.1
Nishigaki, N.2
Washio, Y.3
Kano, K.4
Harris, P.A.5
Sato, H.6
Mori, I.7
West, R.I.8
Shibahara, M.9
Toyoda, H.10
Wang, L.11
Nolte, R.T.12
Veal, J.M.13
Cheung, M.14
|