-
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 (1) 235-242 10.1093/nar/28.1.235
-
(2000)
Nucleic Acids Res.
, vol.28
, Issue.1
, 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
-
-
84875984520
-
Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface
-
Johnson, D. K.; Karanicolas, J. Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface PLoS Comput. Biol. 2013, 9 (3) e1002951 10.1371/journal.pcbi.1002951
-
(2013)
PLoS Comput. Biol.
, vol.9
, Issue.3
, pp. e1002951
-
-
Johnson, D.K.1
Karanicolas, J.2
-
3
-
-
84905454868
-
Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility
-
Loving, K. A.; Lin, A.; Cheng, A. C. Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility PLoS Comput. Biol. 2014, 10 (7) e1003741 10.1371/journal.pcbi.1003741
-
(2014)
PLoS Comput. Biol.
, vol.10
, Issue.7
, pp. e1003741
-
-
Loving, K.A.1
Lin, A.2
Cheng, A.C.3
-
4
-
-
0030777303
-
CATH-a hierarchic classification of protein domain structures
-
Orengo, C. A.; Michie, A. D.; Jones, S.; Jones, D. T.; Swindells, M. B.; Thornton, J. M. CATH-a hierarchic classification of protein domain structures Structure 1997, 5 (8) 1093-1108 10.1016/S0969-2126(97)00260-8
-
(1997)
Structure
, vol.5
, Issue.8
, pp. 1093-1108
-
-
Orengo, C.A.1
Michie, A.D.2
Jones, S.3
Jones, D.T.4
Swindells, M.B.5
Thornton, J.M.6
-
5
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin, A. G.; Brenner, S. E.; Hubbard, T.; Chothia, C. SCOP: a structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 1995, 247 (4) 536-540 10.1016/S0022-2836(05)80134-2
-
(1995)
J. Mol. Biol.
, vol.247
, Issue.4
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
6
-
-
84969550523
-
-
RCSB PDB. (accessed March 21)
-
RCSB PDB. http://www.rcsb.org/pdb/static.do?p=general-information/pdb-statistics/index.html (accessed March 21, 2016).
-
(2016)
-
-
-
7
-
-
84949324877
-
Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function
-
Skolnick, J.; Gao, M.; Roy, A.; Srinivasan, B.; Zhou, H. Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function Bioorg. Med. Chem. Lett. 2015, 25 (6) 1163-1170 10.1016/j.bmcl.2015.01.059
-
(2015)
Bioorg. Med. Chem. Lett.
, vol.25
, Issue.6
, pp. 1163-1170
-
-
Skolnick, J.1
Gao, M.2
Roy, A.3
Srinivasan, B.4
Zhou, H.5
-
8
-
-
1542286205
-
Recovering the true targets of specific ligands by virtual screening of the protein data bank
-
Paul, N.; Kellenberger, E.; Bret, G.; Müller, P.; Rognan, D. Recovering the true targets of specific ligands by virtual screening of the protein data bank Proteins: Struct., Funct., Genet. 2004, 54 (4) 671-680 10.1002/prot.10625
-
(2004)
Proteins: Struct., Funct., Genet.
, vol.54
, Issue.4
, pp. 671-680
-
-
Paul, N.1
Kellenberger, E.2
Bret, G.3
Müller, P.4
Rognan, D.5
-
9
-
-
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.; Rognan, D. sc-PDB: an annotated database of druggable binding sites from the Protein Data Bank J. Chem. Inf. Model. 2006, 46 (2) 717-727 10.1021/ci050372x
-
(2006)
J. Chem. Inf. Model.
, vol.46
, Issue.2
, pp. 717-727
-
-
Kellenberger, E.1
Muller, P.2
Schalon, C.3
Bret, G.4
Foata, N.5
Rognan, D.6
-
10
-
-
84866638168
-
Structural insights into the molecular basis of the ligand promiscuity
-
Sturm, N.; Desaphy, J.; Quinn, R. J.; Rognan, D.; Kellenberger, E. Structural insights into the molecular basis of the ligand promiscuity J. Chem. Inf. Model. 2012, 52 (9) 2410-2421 10.1021/ci300196g
-
(2012)
J. Chem. Inf. Model.
, vol.52
, Issue.9
, pp. 2410-2421
-
-
Sturm, N.1
Desaphy, J.2
Quinn, R.J.3
Rognan, D.4
Kellenberger, E.5
-
11
-
-
44349119204
-
A simple and fuzzy method to align and compare druggable ligand-binding sites
-
Schalon, C.; Surgand, J.-S.; Kellenberger, E.; Rognan, D. A simple and fuzzy method to align and compare druggable ligand-binding sites Proteins: Struct., Funct., Genet. 2008, 71 (4) 1755-1778 10.1002/prot.21858
-
(2008)
Proteins: Struct., Funct., Genet.
, vol.71
, Issue.4
, pp. 1755-1778
-
-
Schalon, C.1
Surgand, J.-S.2
Kellenberger, E.3
Rognan, D.4
-
12
-
-
84865516554
-
Comparison and druggability prediction of protein-ligand binding sites from pharmacophore-annotated cavity shapes
-
Desaphy, J.; Azdimousa, K.; Kellenberger, E.; Rognan, D. Comparison and druggability prediction of protein-ligand binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model. 2012, 52 (8) 2287-2299 10.1021/ci300184x
-
(2012)
J. Chem. Inf. Model.
, vol.52
, Issue.8
, pp. 2287-2299
-
-
Desaphy, J.1
Azdimousa, K.2
Kellenberger, E.3
Rognan, D.4
-
13
-
-
75749155406
-
Alignment-free ultra-high-throughput comparison of druggable protein-ligand binding sites
-
Weill, N.; Rognan, D. Alignment-free ultra-high-throughput comparison of druggable protein-ligand binding sites J. Chem. Inf. Model. 2010, 50 (1) 123-135 10.1021/ci900349y
-
(2010)
J. Chem. Inf. Model.
, vol.50
, Issue.1
, pp. 123-135
-
-
Weill, N.1
Rognan, D.2
-
14
-
-
84969494135
-
-
scPDB: An Annotated Database of Druggable Binding Sites from the Protein DataBank. (accessed March 21)
-
scPDB: An Annotated Database of Druggable Binding Sites from the Protein DataBank. http://cheminfo.u-strasbg.fr/scPDB/ABOUT (accessed March 21, 2016).
-
(2016)
-
-
-
15
-
-
0032527783
-
Protein folds and functions
-
Martin, A. C.; Orengo, C. A.; Hutchinson, E. G.; Jones, S.; Karmirantzou, M.; Laskowski, R. A.; Mitchell, J. B.; Taroni, C.; Thornton, J. M. Protein folds and functions Structure 1998, 6 (7) 875-884 10.1016/S0969-2126(98)00089-6
-
(1998)
Structure
, vol.6
, Issue.7
, pp. 875-884
-
-
Martin, A.C.1
Orengo, C.A.2
Hutchinson, E.G.3
Jones, S.4
Karmirantzou, M.5
Laskowski, R.A.6
Mitchell, J.B.7
Taroni, C.8
Thornton, J.M.9
-
16
-
-
84951852487
-
The recognition of identical ligands by unrelated proteins
-
Barelier, S.; Sterling, T.; OMeara, M. J.; Shoichet, B. K. The recognition of identical ligands by unrelated proteins ACS Chem. Biol. 2015, 10 (12) 2772-2784 10.1021/acschembio.5b00683
-
(2015)
ACS Chem. Biol.
, vol.10
, Issue.12
, pp. 2772-2784
-
-
Barelier, S.1
Sterling, T.2
O'Meara, M.J.3
Shoichet, B.K.4
-
17
-
-
33846876695
-
Relating protein pharmacology by ligand chemistry
-
Keiser, M. J.; Roth, B. L.; Armbruster, B. N.; Ernsberger, P.; Irwin, J. J.; Shoichet, B. K. Relating protein pharmacology by ligand chemistry Nat. Biotechnol. 2007, 25 (2) 197-206 10.1038/nbt1284
-
(2007)
Nat. Biotechnol.
, vol.25
, Issue.2
, pp. 197-206
-
-
Keiser, M.J.1
Roth, B.L.2
Armbruster, B.N.3
Ernsberger, P.4
Irwin, J.J.5
Shoichet, B.K.6
-
18
-
-
84941695617
-
In silico analysis and experimental validation of active compounds from Cichorium intybus L. Ameliorating liver injury
-
Li, G.-Y.; Zheng, Y.-X.; Sun, F.-Z.; Huang, J.; Lou, M.-M.; Gu, J.-K.; Wang, J.-H. In silico analysis and experimental validation of active compounds from Cichorium intybus L. ameliorating liver injury Int. J. Mol. Sci. 2015, 16 (9) 22190-22204 10.3390/ijms160922190
-
(2015)
Int. J. Mol. Sci.
, vol.16
, Issue.9
, pp. 22190-22204
-
-
Li, G.-Y.1
Zheng, Y.-X.2
Sun, F.-Z.3
Huang, J.4
Lou, M.-M.5
Gu, J.-K.6
Wang, J.-H.7
-
19
-
-
84891762026
-
The ChEMBL bioactivity database: An update
-
(Database issue)
-
Bento, A. P.; Gaulton, A.; Hersey, A.; Bellis, L. J.; Chambers, J.; Davies, M.; Krüger, F. A.; Light, Y.; Mak, L.; McGlinchey, S.; Nowotka, M.; Papadatos, G.; Santos, R.; Overington, J. P. The ChEMBL bioactivity database: an update Nucleic Acids Res. 2014, 42 (D1) D1083-D1090 (Database issue) 10.1093/nar/gkt1031
-
(2014)
Nucleic Acids Res.
, vol.42
, Issue.D1
, pp. D1083-D1090
-
-
Bento, A.P.1
Gaulton, A.2
Hersey, A.3
Bellis, L.J.4
Chambers, J.5
Davies, M.6
Krüger, F.A.7
Light, Y.8
Mak, L.9
McGlinchey, S.10
Nowotka, M.11
Papadatos, G.12
Santos, R.13
Overington, J.P.14
-
20
-
-
33644876210
-
DrugBank: A comprehensive resource for in silico drug discovery and exploration
-
(Database issue)
-
Wishart, D. S.; Knox, C.; Guo, A. C.; Shrivastava, S.; Hassanali, M.; Stothard, P.; Chang, Z.; Woolsey, J. DrugBank: a comprehensive resource for in silico drug discovery and exploration Nucleic Acids Res. 2006, 34 (Suppl. 1) D668-D672 (Database issue) 10.1093/nar/gkj067
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. D668-D672
-
-
Wishart, D.S.1
Knox, C.2
Guo, A.C.3
Shrivastava, S.4
Hassanali, M.5
Stothard, P.6
Chang, Z.7
Woolsey, J.8
-
21
-
-
84891805328
-
PubChem BioAssay: 2014 update
-
(Database issue)
-
Wang, Y.; Suzek, T.; Zhang, J.; Wang, J.; He, S.; Cheng, T.; Shoemaker, B. A.; Gindulyte, A.; Bryant, S. H. PubChem BioAssay: 2014 update Nucleic Acids Res. 2014, 42 (D1) D1075-D1082 (Database issue) 10.1093/nar/gkt978
-
(2014)
Nucleic Acids Res.
, vol.42
, Issue.D1
, pp. D1075-D1082
-
-
Wang, Y.1
Suzek, T.2
Zhang, J.3
Wang, J.4
He, S.5
Cheng, T.6
Shoemaker, B.A.7
Gindulyte, A.8
Bryant, S.H.9
-
22
-
-
38549182474
-
SuperTarget and Matador: Resources for exploring drug-target relationships
-
(Database issue)
-
Günther, S.; Kuhn, M.; Dunkel, M.; Campillos, M.; Senger, C.; Petsalaki, E.; Ahmed, J.; Urdiales, E. G.; Gewiess, A.; Jensen, L. J.; Schneider, R.; Skoblo, R.; Russell, R. B.; Bourne, P. E.; Bork, P.; Preissner, R. SuperTarget and Matador: resources for exploring drug-target relationships Nucleic Acids Res. 2008, 36 (Suppl. 1) D919-D922 (Database issue) 10.1093/nar/gkm862
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. D919-D922
-
-
Günther, S.1
Kuhn, M.2
Dunkel, M.3
Campillos, M.4
Senger, C.5
Petsalaki, E.6
Ahmed, J.7
Urdiales, E.G.8
Gewiess, A.9
Jensen, L.J.10
Schneider, R.11
Skoblo, R.12
Russell, R.B.13
Bourne, P.E.14
Bork, P.15
Preissner, R.16
-
23
-
-
84856370676
-
Pocketome: An encyclopedia of small-molecule binding sites in 4D
-
(Database issue)
-
Kufareva, I.; Ilatovskiy, A. V.; Abagyan, R. Pocketome: an encyclopedia of small-molecule binding sites in 4D Nucleic Acids Res. 2012, 40 (D1) D535-D540 (Database issue) 10.1093/nar/gkr825
-
(2012)
Nucleic Acids Res.
, vol.40
, Issue.D1
, pp. D535-D540
-
-
Kufareva, I.1
Ilatovskiy, A.V.2
Abagyan, R.3
-
24
-
-
0031370977
-
LIGSITE: Automatic and efficient detection of potential small molecule-binding sites in proteins
-
Hendlich, M.; Rippmann, F.; Barnickel, G. LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins J. Mol. Graphics Modell. 1997, 15 (6) 359-63, 389 10.1016/S1093-3263(98)00002-3
-
(1997)
J. Mol. Graphics Modell.
, vol.15
, Issue.6
, pp. 359-363
-
-
Hendlich, M.1
Rippmann, F.2
Barnickel, G.3
-
25
-
-
18744394070
-
Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites
-
Laurie, A. T. R.; Jackson, R. M. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites Bioinformatics 2005, 21 (9) 1908-1916 10.1093/bioinformatics/bti315
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 1908-1916
-
-
Laurie, A.T.R.1
Jackson, R.M.2
-
26
-
-
78650788056
-
Prediction of ligand-binding sites of proteins by molecular docking calculation for a random ligand library
-
Fukunishi, Y.; Nakamura, H. Prediction of ligand-binding sites of proteins by molecular docking calculation for a random ligand library Protein Sci. 2011, 20 (1) 95-106 10.1002/pro.540
-
(2011)
Protein Sci.
, vol.20
, Issue.1
, pp. 95-106
-
-
Fukunishi, Y.1
Nakamura, H.2
-
27
-
-
0002218484
-
Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
-
Pupko, T.; Bell, R. E.; Mayrose, I.; Glaser, F.; Ben-Tal, N. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues Bioinformatics 2002, 18 (Suppl. 1) S71-S77 10.1093/bioinformatics/18.suppl-1.S71
-
(2002)
Bioinformatics
, vol.18
, pp. S71-S77
-
-
Pupko, T.1
Bell, R.E.2
Mayrose, I.3
Glaser, F.4
Ben-Tal, N.5
-
28
-
-
69249150494
-
MetaPocket: A meta approach to improve protein ligand binding site prediction
-
Huang, B. MetaPocket: a meta approach to improve protein ligand binding site prediction OMICS 2009, 13 (4) 325-330 10.1089/omi.2009.0045
-
(2009)
OMICS
, vol.13
, Issue.4
, pp. 325-330
-
-
Huang, B.1
-
29
-
-
84921775709
-
Methods for predicting protein-ligand binding sites
-
Xie, Z.-R.; Hwang, M.-J. Methods for predicting protein-ligand binding sites Methods Mol. Biol. 2015, 1215, 383-398 10.1007/978-1-4939-1465-4-17
-
(2015)
Methods Mol. Biol.
, vol.1215
, pp. 383-398
-
-
Xie, Z.-R.1
Hwang, M.-J.2
-
30
-
-
77951210909
-
Mapping of ligand-binding cavities in proteins
-
Andersson, C. D.; Chen, B. Y.; Linusson, A. Mapping of ligand-binding cavities in proteins Proteins: Struct., Funct., Bioinf. 2010, 78 (6) 1408-1422 10.1002/prot.22655
-
(2010)
Proteins: Struct., Funct., Bioinf.
, vol.78
, Issue.6
, pp. 1408-1422
-
-
Andersson, C.D.1
Chen, B.Y.2
Linusson, A.3
-
31
-
-
84865326143
-
Relationship between global structural parameters and Enzyme Commission hierarchy: Implications for function prediction
-
Boareto, M.; Yamagishi, M. E. B.; Caticha, N.; Leite, V. B. P. Relationship between global structural parameters and Enzyme Commission hierarchy: implications for function prediction Comput. Biol. Chem. 2012, 40, 15-19 10.1016/j.compbiolchem.2012.06.003
-
(2012)
Comput. Biol. Chem.
, vol.40
, pp. 15-19
-
-
Boareto, M.1
Yamagishi, M.E.B.2
Caticha, N.3
Leite, V.B.P.4
-
32
-
-
34548317031
-
Chemogenomic approaches to rational drug design
-
Rognan, D. Chemogenomic approaches to rational drug design Br. J. Pharmacol. 2007, 152 (1) 38-52 10.1038/sj.bjp.0707307
-
(2007)
Br. J. Pharmacol.
, vol.152
, Issue.1
, pp. 38-52
-
-
Rognan, D.1
-
33
-
-
84879269767
-
Drug promiscuity in PDB: Protein binding site similarity is key
-
Haupt, V. J.; Daminelli, S.; Schroeder, M. Drug promiscuity in PDB: protein binding site similarity is key PLoS One 2013, 8 (6) e65894 10.1371/journal.pone.0065894
-
(2013)
PLoS One
, vol.8
, Issue.6
, pp. e65894
-
-
Haupt, V.J.1
Daminelli, S.2
Schroeder, M.3
-
34
-
-
84930655650
-
Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations?
-
Bajusz, D.; Rácz, A.; Héberger, K. Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations? J. Cheminf. 2015, 7, 20 10.1186/s13321-015-0069-3
-
(2015)
J. Cheminf.
, vol.7
, pp. 20
-
-
Bajusz, D.1
Rácz, A.2
Héberger, K.3
-
35
-
-
20444409179
-
Protein structure similarity clustering (PSSC) and natural product structure as inspiration sources for drug development and chemical genomics
-
Dekker, F. J.; Koch, M. A.; Waldmann, H. Protein structure similarity clustering (PSSC) and natural product structure as inspiration sources for drug development and chemical genomics Curr. Opin. Chem. Biol. 2005, 9 (3) 232-239 10.1016/j.cbpa.2005.03.003
-
(2005)
Curr. Opin. Chem. Biol.
, vol.9
, Issue.3
, pp. 232-239
-
-
Dekker, F.J.1
Koch, M.A.2
Waldmann, H.3
-
36
-
-
79955953533
-
Use of secondary structure element information in drug design: Polypharmacology and conserved motifs in protein-ligand binding and protein-protein interfaces
-
Koch, O. Use of secondary structure element information in drug design: polypharmacology and conserved motifs in protein-ligand binding and protein-protein interfaces Future Med. Chem. 2011, 3 (6) 699-708 10.4155/fmc.11.26
-
(2011)
Future Med. Chem.
, vol.3
, Issue.6
, pp. 699-708
-
-
Koch, O.1
-
37
-
-
76649139794
-
Computational approaches to identifying and characterizing protein binding sites for ligand design
-
Henrich, S.; Salo-Ahen, O. M. H.; Huang, B.; Rippmann, F. F.; Cruciani, G.; Wade, R. C. Computational approaches to identifying and characterizing protein binding sites for ligand design J. Mol. Recognit. 2010, 23 (2) 209-219 10.1002/jmr.984
-
(2010)
J. Mol. Recognit.
, vol.23
, Issue.2
, pp. 209-219
-
-
Henrich, S.1
Salo-Ahen, O.M.H.2
Huang, B.3
Rippmann, F.F.4
Cruciani, G.5
Wade, R.C.6
-
38
-
-
54749109580
-
How to measure the similarity between protein ligand-binding sites?
-
Kellenberger, E.; Schalon, C.; Rognan, D. How to measure the similarity between protein ligand-binding sites? Curr. Comput.-Aided Drug Des. 2008, 4 (3) 209-220 10.2174/157340908785747401
-
(2008)
Curr. Comput.-Aided Drug Des.
, vol.4
, Issue.3
, pp. 209-220
-
-
Kellenberger, E.1
Schalon, C.2
Rognan, D.3
-
39
-
-
0342645331
-
-
Chemical Computing Group Inc. (1010 Sherbooke St. West, Suite 910, Montreal, QC, H3A 2R7, Canada)
-
MOE (Molecular Operating Environment); Chemical Computing Group Inc. (1010 Sherbooke St. West, Suite 910, Montreal, QC, H3A 2R7, Canada), 2013.
-
(2013)
MOE (Molecular Operating Environment)
-
-
-
40
-
-
10044253102
-
Compound library development guided by protein structure similarity clustering and natural product structure
-
Koch, M. A.; Wittenberg, L.-O.; Basu, S.; Jeyaraj, D. A.; Gourzoulidou, E.; Reinecke, K.; Odermatt, A.; Waldmann, H. Compound library development guided by protein structure similarity clustering and natural product structure Proc. Natl. Acad. Sci. U. S. A. 2004, 101 (48) 16721-16726 10.1073/pnas.0404719101
-
(2004)
Proc. Natl. Acad. Sci. U. S. A.
, vol.101
, Issue.48
, pp. 16721-16726
-
-
Koch, M.A.1
Wittenberg, L.-O.2
Basu, S.3
Jeyaraj, D.A.4
Gourzoulidou, E.5
Reinecke, K.6
Odermatt, A.7
Waldmann, H.8
-
41
-
-
79951526605
-
Ligand binding site superposition and comparison based on Atomic Property Fields: Identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites
-
Totrov, M. Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites BMC Bioinf. 2011, 12 (Suppl. 1) S35 10.1186/1471-2105-12-S1-S35
-
(2011)
BMC Bioinf.
, vol.12
, pp. S35
-
-
Totrov, M.1
-
42
-
-
84937758573
-
Crystal structures of Mycobacterial MeaB and MMAA-like GTPases
-
Edwards, T. E.; Baugh, L.; Bullen, J.; Baydo, R. O.; Witte, P.; Thompkins, K.; Phan, I. Q. H.; Abendroth, J.; Clifton, M. C.; Sankaran, B.; van Voorhis, W. C.; Myler, P. J.; Staker, B. L.; Grundner, C.; Lorimer, D. D. Crystal structures of Mycobacterial MeaB and MMAA-like GTPases J. Struct. Funct. Genomics 2015, 16 (2) 91-99 10.1007/s10969-015-9197-2
-
(2015)
J. Struct. Funct. Genomics
, vol.16
, Issue.2
, pp. 91-99
-
-
Edwards, T.E.1
Baugh, L.2
Bullen, J.3
Baydo, R.O.4
Witte, P.5
Thompkins, K.6
Phan, I.Q.H.7
Abendroth, J.8
Clifton, M.C.9
Sankaran, B.10
Van Voorhis, W.C.11
Myler, P.J.12
Staker, B.L.13
Grundner, C.14
Lorimer, D.D.15
-
43
-
-
84925012277
-
Increasing the structural coverage of tuberculosis drug targets
-
Baugh, L.; Phan, I.; Begley, D. W.; Clifton, M. C.; Armour, B.; Dranow, D. M.; Taylor, B. M.; Muruthi, M. M.; Abendroth, J.; Fairman, J. W.; Fox, D.; Dieterich, S. H.; Staker, B. L.; Gardberg, A. S.; Choi, R.; Hewitt, S. N.; Napuli, A. J.; Myers, J.; Barrett, L. K.; Zhang, Y.; Ferrell, M.; Mundt, E.; Thompkins, K.; Tran, N.; Lyons-Abbott, S.; Abramov, A.; Sekar, A.; Serbzhinskiy, D.; Lorimer, D.; Buchko, G. W.; Stacy, R.; Stewart, L. J.; Edwards, T. E.; van Voorhis, W. C.; Myler, P. J. Increasing the structural coverage of tuberculosis drug targets Tuberculosis 2015, 95 (2) 142-148 10.1016/j.tube.2014.12.003
-
(2015)
Tuberculosis
, vol.95
, Issue.2
, pp. 142-148
-
-
Baugh, L.1
Phan, I.2
Begley, D.W.3
Clifton, M.C.4
Armour, B.5
Dranow, D.M.6
Taylor, B.M.7
Muruthi, M.M.8
Abendroth, J.9
Fairman, J.W.10
Fox, D.11
Dieterich, S.H.12
Staker, B.L.13
Gardberg, A.S.14
Choi, R.15
Hewitt, S.N.16
Napuli, A.J.17
Myers, J.18
Barrett, L.K.19
Zhang, Y.20
Ferrell, M.21
Mundt, E.22
Thompkins, K.23
Tran, N.24
Lyons-Abbott, S.25
Abramov, A.26
Sekar, A.27
Serbzhinskiy, D.28
Lorimer, D.29
Buchko, G.W.30
Stacy, R.31
Stewart, L.J.32
Edwards, T.E.33
Van Voorhis, W.C.34
Myler, P.J.35
more..
-
44
-
-
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. 2002, 323 (2) 387-406 10.1016/S0022-2836(02)00811-2
-
(2002)
J. Mol. Biol.
, vol.323
, Issue.2
, pp. 387-406
-
-
Schmitt, S.1
Kuhn, D.2
Klebe, G.3
-
45
-
-
77949760141
-
Identifying unexpected therapeutic targets via chemical-protein interactome
-
Yang, L.; Chen, J.; Shi, L.; Hudock, M. P.; Wang, K.; He, L. Identifying unexpected therapeutic targets via chemical-protein interactome PLoS One 2010, 5 (3) e9568 10.1371/journal.pone.0009568
-
(2010)
PLoS One
, vol.5
, Issue.3
, pp. e9568
-
-
Yang, L.1
Chen, J.2
Shi, L.3
Hudock, M.P.4
Wang, K.5
He, L.6
-
46
-
-
33745906224
-
An efficient method for the synthesis of peptide aldehyde libraries employed in the discovery of reversible SARS coronavirus main protease (SARS-CoV Mpro) inhibitors
-
Al-Gharabli, S. I.; Shah, S. T. A.; Weik, S.; Schmidt, M. F.; Mesters, J. R.; Kuhn, D.; Klebe, G.; Hilgenfeld, R.; Rademann, J. An efficient method for the synthesis of peptide aldehyde libraries employed in the discovery of reversible SARS coronavirus main protease (SARS-CoV Mpro) inhibitors ChemBioChem 2006, 7 (7) 1048-1055 10.1002/cbic.200500533
-
(2006)
ChemBioChem
, vol.7
, Issue.7
, pp. 1048-1055
-
-
Al-Gharabli, S.I.1
Shah, S.T.A.2
Weik, S.3
Schmidt, M.F.4
Mesters, J.R.5
Kuhn, D.6
Klebe, G.7
Hilgenfeld, R.8
Rademann, J.9
-
47
-
-
33744935012
-
From the similarity analysis of protein cavities to the functional classification of protein families using cavbase
-
Kuhn, D.; Weskamp, N.; Schmitt, S.; Hüllermeier, E.; Klebe, G. From the similarity analysis of protein cavities to the functional classification of protein families using cavbase J. Mol. Biol. 2006, 359 (4) 1023-1044 10.1016/j.jmb.2006.04.024
-
(2006)
J. Mol. Biol.
, vol.359
, Issue.4
, pp. 1023-1044
-
-
Kuhn, D.1
Weskamp, N.2
Schmitt, S.3
Hüllermeier, E.4
Klebe, G.5
-
48
-
-
1642540579
-
Unexpected nanomolar inhibition of carbonic anhydrase by COX-2-selective celecoxib: New pharmacological opportunities due to related binding site recognition
-
Weber, A.; Casini, A.; Heine, A.; Kuhn, D.; Supuran, C. T.; Scozzafava, A.; Klebe, G. Unexpected nanomolar inhibition of carbonic anhydrase by COX-2-selective celecoxib: new pharmacological opportunities due to related binding site recognition J. Med. Chem. 2004, 47 (3) 550-557 10.1021/jm030912m
-
(2004)
J. Med. Chem.
, vol.47
, Issue.3
, pp. 550-557
-
-
Weber, A.1
Casini, A.2
Heine, A.3
Kuhn, D.4
Supuran, C.T.5
Scozzafava, A.6
Klebe, G.7
-
49
-
-
77956525295
-
CMASA: An accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation
-
Li, G.-H.; Huang, J.-F. CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation BMC Bioinf. 2010, 11, 439 10.1186/1471-2105-11-439
-
(2010)
BMC Bioinf.
, vol.11
, pp. 439
-
-
Li, G.-H.1
Huang, J.-F.2
-
50
-
-
84866752887
-
A comparative analysis of protein targets of withdrawn cardiovascular drugs in human and mouse
-
Zhao, Y.; Wang, J.; Wang, Y.; Huang, J. A comparative analysis of protein targets of withdrawn cardiovascular drugs in human and mouse J. Clin. Bioinf. 2012, 2 (1) 10 10.1186/2043-9113-2-10
-
(2012)
J. Clin. Bioinf.
, vol.2
, Issue.1
, pp. 10
-
-
Zhao, Y.1
Wang, J.2
Wang, Y.3
Huang, J.4
-
51
-
-
84864460609
-
COFACTOR: An accurate comparative algorithm for structure-based protein function annotation
-
(Web Server issue)
-
Roy, A.; Yang, J.; Zhang, Y. COFACTOR: an accurate comparative algorithm for structure-based protein function annotation Nucleic Acids Res. 2012, 40 (W1) W471-W477 (Web Server issue) 10.1093/nar/gks372
-
(2012)
Nucleic Acids Res.
, vol.40
, Issue.W1
, pp. W471-W477
-
-
Roy, A.1
Yang, J.2
Zhang, Y.3
-
52
-
-
84941053222
-
Structural bioinformatics inspection of neXtProt PE5 proteins in the human proteome
-
Dong, Q.; Menon, R.; Omenn, G. S.; Zhang, Y. Structural bioinformatics inspection of neXtProt PE5 proteins in the human proteome J. Proteome Res. 2015, 14 (9) 3750-3761 10.1021/acs.jproteome.5b00516
-
(2015)
J. Proteome Res.
, vol.14
, Issue.9
, pp. 3750-3761
-
-
Dong, Q.1
Menon, R.2
Omenn, G.S.3
Zhang, Y.4
-
53
-
-
33748271948
-
Comparison of protein active site structures for functional annotation of proteins and drug design
-
Powers, R.; Copeland, J. C.; Germer, K.; Mercier, K. A.; Ramanathan, V.; Revesz, P. Comparison of protein active site structures for functional annotation of proteins and drug design Proteins: Struct., Funct., Genet. 2006, 65 (1) 124-135 10.1002/prot.21092
-
(2006)
Proteins: Struct., Funct., Genet.
, vol.65
, Issue.1
, pp. 124-135
-
-
Powers, R.1
Copeland, J.C.2
Germer, K.3
Mercier, K.A.4
Ramanathan, V.5
Revesz, P.6
-
54
-
-
77949324326
-
Structural and functional similarity between the bacterial type III secretion system needle protein PrgI and the eukaryotic apoptosis Bcl-2 proteins
-
Shortridge, M. D.; Powers, R. Structural and functional similarity between the bacterial type III secretion system needle protein PrgI and the eukaryotic apoptosis Bcl-2 proteins PLoS One 2009, 4 (10) e7442 10.1371/journal.pone.0007442
-
(2009)
PLoS One
, vol.4
, Issue.10
, pp. e7442
-
-
Shortridge, M.D.1
Powers, R.2
-
55
-
-
0036288284
-
Identification of protein functions from a molecular surface database, eF-site
-
Kinoshita, K.; Furui, J.; Nakamura, H. Identification of protein functions from a molecular surface database, eF-site J. Struct. Funct. Genomics 2002, 2 (1) 9-22 10.1023/A:1011318527094
-
(2002)
J. Struct. Funct. Genomics
, vol.2
, Issue.1
, pp. 9-22
-
-
Kinoshita, K.1
Furui, J.2
Nakamura, H.3
-
56
-
-
0041842509
-
Identification of protein biochemical functions by similarity search using the molecular surface database eF-site
-
Kinoshita, K.; Nakamura, H. Identification of protein biochemical functions by similarity search using the molecular surface database eF-site Protein Sci. 2003, 12 (8) 1589-1595 10.1110/ps.0368703
-
(2003)
Protein Sci.
, vol.12
, Issue.8
, pp. 1589-1595
-
-
Kinoshita, K.1
Nakamura, H.2
-
57
-
-
34247263219
-
A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for Ligands and Proteins (FLAP): Theory and application
-
Baroni, M.; Cruciani, G.; Sciabola, S.; Perruccio, F.; Mason, J. S. A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for Ligands and Proteins (FLAP): theory and application J. Chem. Inf. Model. 2007, 47 (2) 279-294 10.1021/ci600253e
-
(2007)
J. Chem. Inf. Model.
, vol.47
, Issue.2
, pp. 279-294
-
-
Baroni, M.1
Cruciani, G.2
Sciabola, S.3
Perruccio, F.4
Mason, J.S.5
-
58
-
-
75749123456
-
High-throughput virtual screening of proteins using GRID molecular interaction fields
-
Sciabola, S.; Stanton, R. V.; Mills, J. E.; Flocco, M. M.; Baroni, M.; Cruciani, G.; Perruccio, F.; Mason, J. S. High-throughput virtual screening of proteins using GRID molecular interaction fields J. Chem. Inf. Model. 2010, 50 (1) 155-169 10.1021/ci9003317
-
(2010)
J. Chem. Inf. Model.
, vol.50
, Issue.1
, pp. 155-169
-
-
Sciabola, S.1
Stanton, R.V.2
Mills, J.E.3
Flocco, M.M.4
Baroni, M.5
Cruciani, G.6
Perruccio, F.7
Mason, J.S.8
-
59
-
-
75549090058
-
FPOP: Footprinting functional pockets of proteins by comparative spatial patterns
-
(Database issue)
-
Tseng, Y. Y.; Chen, Z. J.; Li, W.-H. fPOP: footprinting functional pockets of proteins by comparative spatial patterns Nucleic Acids Res. 2010, 38 (Suppl. 1) D288-D295 (Database issue) 10.1093/nar/gkp900
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. D288-D295
-
-
Tseng, Y.Y.1
Chen, Z.J.2
Li, W.-H.3
-
60
-
-
84863020006
-
Classification of protein functional surfaces using structural characteristics
-
Tseng, Y. Y.; Li, W.-H. Classification of protein functional surfaces using structural characteristics Proc. Natl. Acad. Sci. U. S. A. 2012, 109 (4) 1170-1175 10.1073/pnas.1119684109
-
(2012)
Proc. Natl. Acad. Sci. U. S. A.
, vol.109
, Issue.4
, pp. 1170-1175
-
-
Tseng, Y.Y.1
Li, W.-H.2
-
61
-
-
33846933784
-
Optimizing fragment and scaffold docking by use of molecular interaction fingerprints
-
Marcou, G.; Rognan, D. Optimizing fragment and scaffold docking by use of molecular interaction fingerprints J. Chem. Inf. Model. 2007, 47 (1) 195-207 10.1021/ci600342e
-
(2007)
J. Chem. Inf. Model.
, vol.47
, Issue.1
, pp. 195-207
-
-
Marcou, G.1
Rognan, D.2
-
62
-
-
84930227130
-
Structure-based prediction of G-protein-coupled receptor ligand function: A β-adrenoceptor case study
-
Kooistra, A. J.; Leurs, R.; de Esch, I. J. P.; de Graaf, C. Structure-based prediction of G-protein-coupled receptor ligand function: a β-adrenoceptor case study J. Chem. Inf. Model. 2015, 55 (5) 1045-1061 10.1021/acs.jcim.5b00066
-
(2015)
J. Chem. Inf. Model.
, vol.55
, Issue.5
, pp. 1045-1061
-
-
Kooistra, A.J.1
Leurs, R.2
De Esch, I.J.P.3
De Graaf, C.4
-
63
-
-
49649083383
-
Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites
-
Najmanovich, R.; Kurbatova, N.; Thornton, J. Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites Bioinformatics 2008, 24 (16) i105-i111 10.1093/bioinformatics/btn263
-
(2008)
Bioinformatics
, vol.24
, Issue.16
, pp. i105-i111
-
-
Najmanovich, R.1
Kurbatova, N.2
Thornton, J.3
-
64
-
-
84964315249
-
A curated C. Difficile strain 630 metabolic network: Prediction of essential targets and inhibitors
-
Larocque, M.; Chénard, T.; Najmanovich, R. A. A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors BMC Syst. Biol. 2014, 8, 117 10.1186/s12918-014-0117-z
-
(2014)
BMC Syst. Biol.
, vol.8
, pp. 117
-
-
Larocque, M.1
Chénard, T.2
Najmanovich, R.A.3
-
65
-
-
84865503111
-
Pharmacophore fingerprint-based approach to binding site subpocket similarity and its application to bioisostere replacement
-
Wood, D. J.; de Vlieg, J.; Wagener, M.; Ritschel, T. Pharmacophore fingerprint-based approach to binding site subpocket similarity and its application to bioisostere replacement J. Chem. Inf. Model. 2012, 52 (8) 2031-2043 10.1021/ci3000776
-
(2012)
J. Chem. Inf. Model.
, vol.52
, Issue.8
, pp. 2031-2043
-
-
Wood, D.J.1
De Vlieg, J.2
Wagener, M.3
Ritschel, T.4
-
66
-
-
84942627515
-
Mitochondrial ADP/ATP exchange inhibition: A novel off-target mechanism underlying ibipinabant-induced myotoxicity
-
Schirris, T. J. J.; Ritschel, T.; Herma Renkema, G.; Willems; Peter, H. G. M.; Smeitink, J. A. M.; Russel, F. G. M. Mitochondrial ADP/ATP exchange inhibition: a novel off-target mechanism underlying ibipinabant-induced myotoxicity Sci. Rep. 2015, 5, 14533 10.1038/srep14533
-
(2015)
Sci. Rep.
, vol.5
, pp. 14533
-
-
Schirris, T.J.J.1
Ritschel, T.2
Herma Renkema, G.3
Willems4
Peter, H.G.M.5
Smeitink, J.A.M.6
Russel, F.G.M.7
-
67
-
-
3042809615
-
Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: An automated all-against-all structural comparison using geometric matching
-
Brakoulias, A.; Jackson, R. M. Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching Proteins: Struct., Funct., Genet. 2004, 56 (2) 250-260 10.1002/prot.20123
-
(2004)
Proteins: Struct., Funct., Genet.
, vol.56
, Issue.2
, pp. 250-260
-
-
Brakoulias, A.1
Jackson, R.M.2
-
68
-
-
65249170904
-
Binding site similarity analysis for the functional classification of the protein kinase family
-
Kinnings, S. L.; Jackson, R. M. Binding site similarity analysis for the functional classification of the protein kinase family J. Chem. Inf. Model. 2009, 49 (2) 318-329 10.1021/ci800289y
-
(2009)
J. Chem. Inf. Model.
, vol.49
, Issue.2
, pp. 318-329
-
-
Kinnings, S.L.1
Jackson, R.M.2
-
69
-
-
77955814959
-
A structural-alphabet-based strategy for finding structural motifs across protein families
-
Wu, C. Y.; Chen, Y. C.; Lim, C. A structural-alphabet-based strategy for finding structural motifs across protein families Nucleic Acids Res. 2010, 38 (14) e150 10.1093/nar/gkq478
-
(2010)
Nucleic Acids Res.
, vol.38
, Issue.14
, pp. e150
-
-
Wu, C.Y.1
Chen, Y.C.2
Lim, C.3
-
70
-
-
84923377191
-
Sequence-motif detection of NAD(P)-binding proteins: Discovery of a unique antibacterial drug target
-
Hua, Y. H.; Wu, C. Y.; Sargsyan, K.; Lim, C. Sequence-motif detection of NAD(P)-binding proteins: discovery of a unique antibacterial drug target Sci. Rep. 2014, 4, 6471 10.1038/srep06471
-
(2014)
Sci. Rep.
, vol.4
, pp. 6471
-
-
Hua, Y.H.1
Wu, C.Y.2
Sargsyan, K.3
Lim, C.4
-
71
-
-
73349097886
-
Rapid comparison of protein binding site surfaces with property encoded shape distributions
-
Das, S.; Kokardekar, A.; Breneman, C. M. Rapid comparison of protein binding site surfaces with property encoded shape distributions J. Chem. Inf. Model. 2009, 49 (12) 2863-2872 10.1021/ci900317x
-
(2009)
J. Chem. Inf. Model.
, vol.49
, Issue.12
, pp. 2863-2872
-
-
Das, S.1
Kokardekar, A.2
Breneman, C.M.3
-
72
-
-
77649229098
-
Binding affinity prediction with property-encoded shape distribution signatures
-
Das, S.; Krein, M. P.; Breneman, C. M. Binding affinity prediction with property-encoded shape distribution signatures J. Chem. Inf. Model. 2010, 50 (2) 298-308 10.1021/ci9004139
-
(2010)
J. Chem. Inf. Model.
, vol.50
, Issue.2
, pp. 298-308
-
-
Das, S.1
Krein, M.P.2
Breneman, C.M.3
-
73
-
-
84855286318
-
Using multiple microenvironments to find similar ligand-binding sites: Application to kinase inhibitor binding
-
Liu, T.; Altman, R. B. Using multiple microenvironments to find similar ligand-binding sites: application to kinase inhibitor binding PLoS Comput. Biol. 2011, 7 (12) e1002326 10.1371/journal.pcbi.1002326
-
(2011)
PLoS Comput. Biol.
, vol.7
, Issue.12
, pp. e1002326
-
-
Liu, T.1
Altman, R.B.2
-
74
-
-
84926335263
-
Variations in the binding pocket of an inhibitor of the bacterial division protein FtsZ across genotypes and species
-
Miguel, A.; Hsin, J.; Liu, T.; Tang, G.; Altman, R. B.; Huang, K. C. Variations in the binding pocket of an inhibitor of the bacterial division protein FtsZ across genotypes and species PLoS Comput. Biol. 2015, 11 (3) e1004117 10.1371/journal.pcbi.1004117
-
(2015)
PLoS Comput. Biol.
, vol.11
, Issue.3
, pp. e1004117
-
-
Miguel, A.1
Hsin, J.2
Liu, T.3
Tang, G.4
Altman, R.B.5
Huang, K.C.6
-
75
-
-
60649117152
-
PocketMatch: A new algorithm to compare binding sites in protein structures
-
Yeturu, K.; Chandra, N. PocketMatch: a new algorithm to compare binding sites in protein structures BMC Bioinf. 2008, 9, 543 10.1186/1471-2105-9-543
-
(2008)
BMC Bioinf.
, vol.9
, pp. 543
-
-
Yeturu, K.1
Chandra, N.2
-
76
-
-
80055119135
-
Structural annotation of Mycobacterium tuberculosis proteome
-
Anand, P.; Sankaran, S.; Mukherjee, S.; Yeturu, K.; Laskowski, R.; Bhardwaj, A.; Bhagavat, R.; Brahmachari, S. K.; Chandra, N. Structural annotation of Mycobacterium tuberculosis proteome PLoS One 2011, 6 (10) e27044 10.1371/journal.pone.0027044
-
(2011)
PLoS One
, vol.6
, Issue.10
, pp. e27044
-
-
Anand, P.1
Sankaran, S.2
Mukherjee, S.3
Yeturu, K.4
Laskowski, R.5
Bhardwaj, A.6
Bhagavat, R.7
Brahmachari, S.K.8
Chandra, N.9
-
77
-
-
84941978806
-
Similarities between the binding sites of SB-206553 at serotonin type 2 and alpha7 acetylcholine nicotinic receptors: Rationale for its polypharmacological profile
-
Möller-Acuna, P.; Contreras-Riquelme, J. S.; Rojas-Fuentes, C.; Nunez-Vivanco, G.; Alzate-Morales, J.; Iturriaga-Vásquez, P.; Arias, H. R.; Reyes-Parada, M. Similarities between the binding sites of SB-206553 at serotonin type 2 and alpha7 acetylcholine nicotinic receptors: rationale for its polypharmacological profile PLoS One 2015, 10 (8) e0134444 10.1371/journal.pone.0134444
-
(2015)
PLoS One
, vol.10
, Issue.8
, pp. e0134444
-
-
Möller-Acuna, P.1
Contreras-Riquelme, J.S.2
Rojas-Fuentes, C.3
Nunez-Vivanco, G.4
Alzate-Morales, J.5
Iturriaga-Vásquez, P.6
Arias, H.R.7
Reyes-Parada, M.8
-
78
-
-
84908137477
-
Similarities between the binding sites of monoamine oxidase (MAO) from different species-Is zebrafish a useful model for the discovery of novel MAO inhibitors?
-
Radis-Baptista, G. InTech, DOI
-
Fierro, A.; Montecinos, A.; Gmez-Molina, C.; Nez, G.; Aldeco, M.; Edmondson, D. E.; Vilches Herrera, M.; Luhr, S.; Iturriaga-Vsquez, P.; Reyes Par, M. Similarities between the binding sites of monoamine oxidase (MAO) from different species-Is zebrafish a useful model for the discovery of novel MAO inhibitors? In An Integrated View of the Molecular Recognition and Toxinology: From Analytical Procedures to Biomedical Applications; Radis-Baptista, G., Ed.; InTech, 2013; DOI: 10.5772/35874.
-
(2013)
An Integrated View of the Molecular Recognition and Toxinology: From Analytical Procedures to Biomedical Applications
-
-
Fierro, A.1
Montecinos, A.2
Gmez-Molina, C.3
Nez, G.4
Aldeco, M.5
Edmondson, D.E.6
Vilches Herrera, M.7
Luhr, S.8
Iturriaga-Vsquez, P.9
Reyes Par, M.10
-
79
-
-
78649849859
-
Self-organizing fuzzy graphs for structure-based comparison of protein pockets
-
Reisen, F.; Weisel, M.; Kriegl, J. M.; Schneider, G. Self-organizing fuzzy graphs for structure-based comparison of protein pockets J. Proteome Res. 2010, 9 (12) 6498-6510 10.1021/pr100719n
-
(2010)
J. Proteome Res.
, vol.9
, Issue.12
, pp. 6498-6510
-
-
Reisen, F.1
Weisel, M.2
Kriegl, J.M.3
Schneider, G.4
-
80
-
-
84942939433
-
In silico adoption of an orphan nuclear receptor NR4A1
-
Lanig, H.; Reisen, F.; Whitley, D.; Schneider, G.; Banting, L.; Clark, T. In silico adoption of an orphan nuclear receptor NR4A1 PLoS One 2015, 10 (8) e0135246 10.1371/journal.pone.0135246
-
(2015)
PLoS One
, vol.10
, Issue.8
, pp. e0135246
-
-
Lanig, H.1
Reisen, F.2
Whitley, D.3
Schneider, G.4
Banting, L.5
Clark, T.6
-
81
-
-
77952849162
-
ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment
-
Konc, J.; Janežič, D. ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment Bioinformatics 2010, 26 (9) 1160-1168 10.1093/bioinformatics/btq100
-
(2010)
Bioinformatics
, vol.26
, Issue.9
, pp. 1160-1168
-
-
Konc, J.1
Janežič, D.2
-
82
-
-
84888226422
-
Structure-based function prediction of uncharacterized protein using binding sites comparison
-
Konc, J.; Hodošček, M.; Ogrizek, M.; Trykowska Konc, J.; Janežič, D. Structure-based function prediction of uncharacterized protein using binding sites comparison PLoS Comput. Biol. 2013, 9 (11) e1003341 10.1371/journal.pcbi.1003341
-
(2013)
PLoS Comput. Biol.
, vol.9
, Issue.11
, pp. e1003341
-
-
Konc, J.1
Hodošček, M.2
Ogrizek, M.3
Trykowska Konc, J.4
Janežič, D.5
-
83
-
-
84938795420
-
A novel antiviral target structure involved in the RNA binding, dimerization, and nuclear export functions of the influenza A virus nucleoprotein
-
Kakisaka, M.; Sasaki, Y.; Yamada, K.; Kondoh, Y.; Hikono, H.; Osada, H.; Tomii, K.; Saito, T.; Aida, Y. A novel antiviral target structure involved in the RNA binding, dimerization, and nuclear export functions of the influenza A virus nucleoprotein PLoS Pathog. 2015, 11 (7) e1005062 10.1371/journal.ppat.1005062
-
(2015)
PLoS Pathog.
, vol.11
, Issue.7
, pp. e1005062
-
-
Kakisaka, M.1
Sasaki, Y.2
Yamada, K.3
Kondoh, Y.4
Hikono, H.5
Osada, H.6
Tomii, K.7
Saito, T.8
Aida, Y.9
-
84
-
-
80051567982
-
Surface-based protein binding pocket similarity
-
Spitzer, R.; Cleves, A. E.; Jain, A. N. Surface-based protein binding pocket similarity Proteins: Struct., Funct., Genet. 2011, 79 (9) 2746-2763 10.1002/prot.23103
-
(2011)
Proteins: Struct., Funct., Genet.
, vol.79
, Issue.9
, pp. 2746-2763
-
-
Spitzer, R.1
Cleves, A.E.2
Jain, A.N.3
-
85
-
-
84922104999
-
Chemical and protein structural basis for biological crosstalk between PPARα and COX enzymes
-
Cleves, A. E.; Jain, A. N. Chemical and protein structural basis for biological crosstalk between PPARα and COX enzymes J. Comput.-Aided Mol. Des. 2015, 29 (2) 101-112 10.1007/s10822-014-9815-2
-
(2015)
J. Comput.-Aided Mol. Des.
, vol.29
, Issue.2
, pp. 101-112
-
-
Cleves, A.E.1
Jain, A.N.2
-
86
-
-
33947201695
-
Query3d: A new method for high-throughput analysis of functional residues in protein structures
-
Ausiello, G.; Via, A.; Helmer-Citterich, M. Query3d: a new method for high-throughput analysis of functional residues in protein structures BMC Bioinf. 2005, 6 (Suppl. 4) S5 10.1186/1471-2105-6-S4-S5
-
(2005)
BMC Bioinf.
, vol.6
, pp. S5
-
-
Ausiello, G.1
Via, A.2
Helmer-Citterich, M.3
-
87
-
-
34248185418
-
Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites
-
Ausiello, G.; Peluso, D.; Via, A.; Helmer-Citterich, M. Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites BMC Bioinf. 2007, 8 (Suppl. 1) S24 10.1186/1471-2105-8-S1-S24
-
(2007)
BMC Bioinf.
, vol.8
, pp. S24
-
-
Ausiello, G.1
Peluso, D.2
Via, A.3
Helmer-Citterich, M.4
-
88
-
-
77957857557
-
Binding of protein kinase inhibitors to synapsin i inferred from pair-wise binding site similarity measurements
-
De Franchi, E.; Schalon, C.; Messa, M.; Onofri, F.; Benfenati, F.; Rognan, D. Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements PLoS One 2010, 5 (8) e12214 10.1371/journal.pone.0012214
-
(2010)
PLoS One
, vol.5
, Issue.8
, pp. e12214
-
-
De Franchi, E.1
Schalon, C.2
Messa, M.3
Onofri, F.4
Benfenati, F.5
Rognan, D.6
-
89
-
-
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 (3) 607-633 10.1016/j.jmb.2004.04.012
-
(2004)
J. Mol. Biol.
, vol.339
, Issue.3
, pp. 607-633
-
-
Shulman-Peleg, A.1
Nussinov, R.2
Wolfson, H.J.3
-
90
-
-
84875213020
-
Structure-based in silico identification of ubiquitin-binding domains provides insights into the ALIX-V:ubiquitin complex and retrovirus budding
-
Keren-Kaplan, T.; Attali, I.; Estrin, M.; Kuo, L. S.; Farkash, E.; Jerabek-Willemsen, M.; Blutraich, N.; Artzi, S.; Peri, A.; Freed, E. O.; Wolfson, H. J.; Prag, G. Structure-based in silico identification of ubiquitin-binding domains provides insights into the ALIX-V:ubiquitin complex and retrovirus budding EMBO J. 2013, 32 (4) 538-551 10.1038/emboj.2013.4
-
(2013)
EMBO J.
, vol.32
, Issue.4
, pp. 538-551
-
-
Keren-Kaplan, T.1
Attali, I.2
Estrin, M.3
Kuo, L.S.4
Farkash, E.5
Jerabek-Willemsen, M.6
Blutraich, N.7
Artzi, S.8
Peri, A.9
Freed, E.O.10
Wolfson, H.J.11
Prag, G.12
-
91
-
-
66349119013
-
A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery
-
Xie, L.; Xie, L.; Bourne, P. E. A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery Bioinformatics 2009, 25 (12) i305-i312 10.1093/bioinformatics/btp220
-
(2009)
Bioinformatics
, vol.25
, Issue.12
, pp. i305-i312
-
-
Xie, L.1
Xie, L.2
Bourne, P.E.3
-
92
-
-
79955562721
-
Drug discovery using chemical systems biology: Weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir
-
Xie, L.; Evangelidis, T.; Xie, L.; Bourne, P. E. Drug discovery using chemical systems biology: weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir PLoS Comput. Biol. 2011, 7 (4) e1002037 10.1371/journal.pcbi.1002037
-
(2011)
PLoS Comput. Biol.
, vol.7
, Issue.4
, pp. e1002037
-
-
Xie, L.1
Evangelidis, T.2
Xie, L.3
Bourne, P.E.4
-
93
-
-
84891487225
-
Structural bioinformatics-based identification of EGFR inhibitor gefitinib as a putative lead compound for BACE
-
Niu, M.; Hu, J.; Wu, S.; Xiaoe, Z.; Xu, H.; Zhang, Y.; Zhang, J.; Yang, Y. Structural bioinformatics-based identification of EGFR inhibitor gefitinib as a putative lead compound for BACE Chem. Biol. Drug Des. 2014, 83 (1) 81-88 10.1111/cbdd.12200
-
(2014)
Chem. Biol. Drug Des.
, vol.83
, Issue.1
, pp. 81-88
-
-
Niu, M.1
Hu, J.2
Wu, S.3
Xiaoe, Z.4
Xu, H.5
Zhang, Y.6
Zhang, J.7
Yang, Y.8
-
94
-
-
44449139387
-
Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments
-
Xie, L.; Bourne, P. E. Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments Proc. Natl. Acad. Sci. U. S. A. 2008, 105 (14) 5441-5446 10.1073/pnas.0704422105
-
(2008)
Proc. Natl. Acad. Sci. U. S. A.
, vol.105
, Issue.14
, pp. 5441-5446
-
-
Xie, L.1
Bourne, P.E.2
-
95
-
-
68249144628
-
Drug discovery using chemical systems biology: Repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis
-
Kinnings, S. L.; Liu, N.; Buchmeier, N.; Tonge, P. J.; Xie, L.; Bourne, P. E. Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis PLoS Comput. Biol. 2009, 5 (7) e1000423 10.1371/journal.pcbi.1000423
-
(2009)
PLoS Comput. Biol.
, vol.5
, Issue.7
, pp. e1000423
-
-
Kinnings, S.L.1
Liu, N.2
Buchmeier, N.3
Tonge, P.J.4
Xie, L.5
Bourne, P.E.6
-
96
-
-
36949009488
-
In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators
-
Xie, L.; Wang, J.; Bourne, P. E. In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators PLoS Comput. Biol. 2007, 3 (11) e217 10.1371/journal.pcbi.0030217
-
(2007)
PLoS Comput. Biol.
, vol.3
, Issue.11
, pp. e217
-
-
Xie, L.1
Wang, J.2
Bourne, P.E.3
-
97
-
-
58349103124
-
Protein functional surfaces: Global shape matching and local spatial alignments of ligand binding sites
-
Binkowski, T. A.; Joachimiak, A. Protein functional surfaces: global shape matching and local spatial alignments of ligand binding sites BMC Struct. Biol. 2008, 8, 45 10.1186/1472-6807-8-45
-
(2008)
BMC Struct. Biol.
, vol.8
, pp. 45
-
-
Binkowski, T.A.1
Joachimiak, A.2
-
98
-
-
78651083184
-
A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair
-
Babu, M.; Beloglazova, N.; Flick, R.; Graham, C.; Skarina, T.; Nocek, B.; Gagarinova, A.; Pogoutse, O.; Brown, G.; Binkowski, A.; Phanse, S.; Joachimiak, A.; Koonin, E. V.; Savchenko, A.; Emili, A.; Greenblatt, J.; Edwards, A. M.; Yakunin, A. F. A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair Mol. Microbiol. 2011, 79 (2) 484-502 10.1111/j.1365-2958.2010.07465.x
-
(2011)
Mol. Microbiol.
, vol.79
, Issue.2
, pp. 484-502
-
-
Babu, M.1
Beloglazova, N.2
Flick, R.3
Graham, C.4
Skarina, T.5
Nocek, B.6
Gagarinova, A.7
Pogoutse, O.8
Brown, G.9
Binkowski, A.10
Phanse, S.11
Joachimiak, A.12
Koonin, E.V.13
Savchenko, A.14
Emili, A.15
Greenblatt, J.16
Edwards, A.M.17
Yakunin, A.F.18
-
99
-
-
17644392830
-
TM-align: A protein structure alignment algorithm based on the TM-score
-
Zhang, Y.; Skolnick, J. TM-align: a protein structure alignment algorithm based on the TM-score Nucleic Acids Res. 2005, 33 (7) 2302-2309 10.1093/nar/gki524
-
(2005)
Nucleic Acids Res.
, vol.33
, Issue.7
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
100
-
-
84928104493
-
Computational discovery and experimental verification of tyrosine kinase inhibitor pazopanib for the reversal of memory and cognitive deficits in rat model neurodegeneration
-
Yang, Y.; Li, G.; Zhao, D.; Yu, H.; Zheng, X.; Peng, X.; Zhang, X.; Fu, T.; Hu, X.; Niu, M.; Ji, X.; Zou, L.; Wang, J. Computational discovery and experimental verification of tyrosine kinase inhibitor pazopanib for the reversal of memory and cognitive deficits in rat model neurodegeneration Chem. Sci. 2015, 6 (5) 2812-2821 10.1039/C4SC03416C
-
(2015)
Chem. Sci.
, vol.6
, Issue.5
, pp. 2812-2821
-
-
Yang, Y.1
Li, G.2
Zhao, D.3
Yu, H.4
Zheng, X.5
Peng, X.6
Zhang, X.7
Fu, T.8
Hu, X.9
Niu, M.10
Ji, X.11
Zou, L.12
Wang, J.13
-
101
-
-
0021871375
-
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
-
Goodford, P. J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules J. Med. Chem. 1985, 28 (7) 849-857 10.1021/jm00145a002
-
(1985)
J. Med. Chem.
, vol.28
, Issue.7
, pp. 849-857
-
-
Goodford, P.J.1
-
102
-
-
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) 1466-1475 10.1021/ci100210c
-
(2010)
J. Chem. Inf. Model.
, vol.50
, Issue.8
, pp. 1466-1475
-
-
Feldman, H.J.1
Labute, P.2
-
103
-
-
0034669774
-
Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks
-
de Brevern, A. G.; Etchebest, C.; Hazout, S. Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks Proteins: Struct., Funct., Bioinf. 2000, 41 (3) 271-287 10.1002/1097-0134(20001115)41:3<271::AID-PROT10>3.0.CO;2-Z
-
(2000)
Proteins: Struct., Funct., Bioinf.
, vol.41
, Issue.3
, pp. 271-287
-
-
De Brevern, A.G.1
Etchebest, C.2
Hazout, S.3
-
104
-
-
37849034064
-
Atomic property fields: Generalized 3D pharmacophoric potential for automated ligand superposition, pharmacophore elucidation and 3D QSAR
-
Totrov, M. Atomic property fields: generalized 3D pharmacophoric potential for automated ligand superposition, pharmacophore elucidation and 3D QSAR Chem. Biol. Drug Des. 2008, 71 (1) 15-27 10.1111/j.1747-0285.2007.00605.x
-
(2008)
Chem. Biol. Drug Des.
, vol.71
, Issue.1
, pp. 15-27
-
-
Totrov, M.1
-
105
-
-
0033969620
-
Morphological similarity: A 3D molecular similarity method correlated with protein-ligand recognition
-
Jain, A. N. Morphological similarity: a 3D molecular similarity method correlated with protein-ligand recognition J. Comput.-Aided Mol. Des. 2000, 14 (2) 199-213 10.1023/A:1008100132405
-
(2000)
J. Comput.-Aided Mol. Des.
, vol.14
, Issue.2
, pp. 199-213
-
-
Jain, A.N.1
-
106
-
-
84895552691
-
Protein function annotation by local binding site surface similarity
-
Spitzer, R.; Cleves, A. E.; Varela, R.; Jain, A. N. Protein function annotation by local binding site surface similarity Proteins: Struct., Funct., Genet. 2014, 82 (4) 679-694 10.1002/prot.24450
-
(2014)
Proteins: Struct., Funct., Genet.
, vol.82
, Issue.4
, pp. 679-694
-
-
Spitzer, R.1
Cleves, A.E.2
Varela, R.3
Jain, A.N.4
-
107
-
-
0037436339
-
Relibase: Design and development of a database for comprehensive analysis of protein-ligand interactions
-
Hendlich, M.; Bergner, A.; Günther, J.; Klebe, G. Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions J. Mol. Biol. 2003, 326 (2) 607-620 10.1016/S0022-2836(02)01408-0
-
(2003)
J. Mol. Biol.
, vol.326
, Issue.2
, pp. 607-620
-
-
Hendlich, M.1
Bergner, A.2
Günther, J.3
Klebe, G.4
-
108
-
-
0037436333
-
Utilising structural knowledge in drug design strategies: Applications using Relibase
-
Günther, J.; Bergner, A.; Hendlich, M.; Klebe, G. Utilising structural knowledge in drug design strategies: applications using Relibase J. Mol. Biol. 2003, 326 (2) 621-636 10.1016/S0022-2836(02)01409-2
-
(2003)
J. Mol. Biol.
, vol.326
, Issue.2
, pp. 621-636
-
-
Günther, J.1
Bergner, A.2
Hendlich, M.3
Klebe, G.4
-
109
-
-
0028881975
-
SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
-
Laskowski, R. A. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions J. Mol. Graphics 1995, 13 (5) 323-330, 307-308 10.1016/0263-7855(95)00073-9
-
(1995)
J. Mol. Graphics
, vol.13
, Issue.5
, pp. 323-330
-
-
Laskowski, R.A.1
-
110
-
-
12944257228
-
The ConSurf-HSSP database: The mapping of evolutionary conservation among homologs onto PDB structures
-
Glaser, F.; Rosenberg, Y.; Kessel, A.; Pupko, T.; Ben-Tal, N. The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures Proteins: Struct., Funct., Genet. 2005, 58 (3) 610-617 10.1002/prot.20305
-
(2005)
Proteins: Struct., Funct., Genet.
, vol.58
, Issue.3
, pp. 610-617
-
-
Glaser, F.1
Rosenberg, Y.2
Kessel, A.3
Pupko, T.4
Ben-Tal, N.5
-
111
-
-
0015505473
-
Repeating sequences and gene duplication in proteins
-
McLachlan, A. D. Repeating sequences and gene duplication in proteins J. Mol. Biol. 1972, 64 (2) 417-437 10.1016/0022-2836(72)90508-6
-
(1972)
J. Mol. Biol.
, vol.64
, Issue.2
, pp. 417-437
-
-
McLachlan, A.D.1
-
112
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff, S.; Henikoff, J. G. Amino acid substitution matrices from protein blocks Proc. Natl. Acad. Sci. U. S. A. 1992, 89 (22) 10915-10919 10.1073/pnas.89.22.10915
-
(1992)
Proc. Natl. Acad. Sci. U. S. A.
, vol.89
, Issue.22
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
113
-
-
35348992193
-
An improved branch and bound algorithm for the maximum clique problem
-
Konc, J.; Janežič, D. An improved branch and bound algorithm for the maximum clique problem MATCH 2007, 58, 569-590
-
(2007)
MATCH
, vol.58
, pp. 569-590
-
-
Konc, J.1
Janežič, D.2
-
114
-
-
0042890523
-
Inferring functional relationships of proteins from local sequence and spatial surface patterns
-
Binkowski, T. A.; Adamian, L.; Liang, J. Inferring functional relationships of proteins from local sequence and spatial surface patterns J. Mol. Biol. 2003, 332 (2) 505-526 10.1016/S0022-2836(03)00882-9
-
(2003)
J. Mol. Biol.
, vol.332
, Issue.2
, pp. 505-526
-
-
Binkowski, T.A.1
Adamian, L.2
Liang, J.3
-
115
-
-
0041989751
-
CASTp: Computed Atlas of Surface Topography of proteins
-
Binkowski, T. A.; Naghibzadeh, S.; Liang, J. CASTp: Computed Atlas of Surface Topography of proteins Nucleic Acids Res. 2003, 31 (13) 3352-3355 10.1093/nar/gkg512
-
(2003)
Nucleic Acids Res.
, vol.31
, Issue.13
, pp. 3352-3355
-
-
Binkowski, T.A.1
Naghibzadeh, S.2
Liang, J.3
-
116
-
-
0025950944
-
Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms
-
Pearson, W. R. Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms Genomics 1991, 11 (3) 635-650 10.1016/0888-7543(91)90071-L
-
(1991)
Genomics
, vol.11
, Issue.3
, pp. 635-650
-
-
Pearson, W.R.1
-
117
-
-
23144456254
-
SiteEngines: Recognition and comparison of binding sites and protein-protein interfaces
-
(Web Server issue)
-
Shulman-Peleg, A.; Nussinov, R.; Wolfson, H. J. SiteEngines: recognition and comparison of binding sites and protein-protein interfaces Nucleic Acids Res. 2005, 33 (Suppl. 2) W337-W341 (Web Server issue) 10.1093/nar/gki482
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. W337-W341
-
-
Shulman-Peleg, A.1
Nussinov, R.2
Wolfson, H.J.3
-
118
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch, W.; Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 1983, 22 (12) 2577-2637 10.1002/bip.360221211
-
(1983)
Biopolymers
, vol.22
, Issue.12
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
119
-
-
0242720595
-
The PDB is a covering set of small protein structures
-
Kihara, D.; Skolnick, J. The PDB is a covering set of small protein structures J. Mol. Biol. 2003, 334 (4) 793-802 10.1016/j.jmb.2003.10.027
-
(2003)
J. Mol. Biol.
, vol.334
, Issue.4
, pp. 793-802
-
-
Kihara, D.1
Skolnick, J.2
-
120
-
-
0000228203
-
A model of evolutionary change in proteins
-
Dayhoff, M. O. National Biomedical Research Foundation: Washington, DC
-
Dayhoff, M. O.; Schwartz, R. M.; Orcutt, B. C. A model of evolutionary change in proteins. In Atlas of Protein Sequence and Structure; Dayhoff, M. O., Ed.; National Biomedical Research Foundation: Washington, DC, 1978; pp 345-352.
-
(1978)
Atlas of Protein Sequence and Structure
, pp. 345-352
-
-
Dayhoff, M.O.1
Schwartz, R.M.2
Orcutt, B.C.3
-
121
-
-
67849111559
-
SplitPocket: Identification of protein functional surfaces and characterization of their spatial patterns
-
(Web Server issue)
-
Tseng, Y. Y.; Dupree, C.; Chen, Z. J.; Li, W.-H. SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns Nucleic Acids Res. 2009, 37 (Suppl. 2) W384-W389 (Web Server issue) 10.1093/nar/gkp308
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. W384-W389
-
-
Tseng, Y.Y.1
Dupree, C.2
Chen, Z.J.3
Li, W.-H.4
-
122
-
-
0031306229
-
Using the radial distributions of physical features to compare amino acid environments and align amino acid sequences
-
Wei, L.; Altman, R. B.; Chang, J. T. Using the radial distributions of physical features to compare amino acid environments and align amino acid sequences Pac. Symp. Biocomput. 1997, 465-476
-
(1997)
Pac. Symp. Biocomput.
, pp. 465-476
-
-
Wei, L.1
Altman, R.B.2
Chang, J.T.3
-
123
-
-
34447637608
-
Clustering protein environments for function prediction: Finding PROSITE motifs in 3D
-
Yoon, S.; Ebert, J. C.; Chung, E.-Y.; De Micheli, G.; Altman, R. B. Clustering protein environments for function prediction: finding PROSITE motifs in 3D BMC Bioinf. 2007, 8 (Suppl. 4) S10 10.1186/1471-2105-8-S4-S10
-
(2007)
BMC Bioinf.
, vol.8
, pp. S10
-
-
Yoon, S.1
Ebert, J.C.2
Chung, E.-Y.3
De Micheli, G.4
Altman, R.B.5
-
124
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
Shindyalov, I. N.; Bourne, P. E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path Protein Eng., Des. Sel. 1998, 11 (9) 739-747 10.1093/protein/11.9.739
-
(1998)
Protein Eng., Des. Sel.
, vol.11
, Issue.9
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
125
-
-
0029894013
-
The properties of known drugs. 1. Molecular frameworks
-
Bemis, G. W.; Murcko, M. A. The properties of known drugs. 1. Molecular frameworks J. Med. Chem. 1996, 39 (15) 2887-2893 10.1021/jm9602928
-
(1996)
J. Med. Chem.
, vol.39
, Issue.15
, pp. 2887-2893
-
-
Bemis, G.W.1
Murcko, M.A.2
-
126
-
-
77955026641
-
PESDserv: A server for high-throughput comparison of protein binding site surfaces
-
Das, S.; Krein, M. P.; Breneman, C. M. PESDserv: a server for high-throughput comparison of protein binding site surfaces Bioinformatics 2010, 26 (15) 1913-1914 10.1093/bioinformatics/btq288
-
(2010)
Bioinformatics
, vol.26
, Issue.15
, pp. 1913-1914
-
-
Das, S.1
Krein, M.P.2
Breneman, C.M.3
-
127
-
-
80054851231
-
Peptide aldehyde inhibitors challenge the substrate specificity of the SARS-coronavirus main protease
-
Zhu, L.; George, S.; Schmidt, M. F.; Al-Gharabli, S. I.; Rademann, J.; Hilgenfeld, R. Peptide aldehyde inhibitors challenge the substrate specificity of the SARS-coronavirus main protease Antiviral Res. 2011, 92 (2) 204-212 10.1016/j.antiviral.2011.08.001
-
(2011)
Antiviral Res.
, vol.92
, Issue.2
, pp. 204-212
-
-
Zhu, L.1
George, S.2
Schmidt, M.F.3
Al-Gharabli, S.I.4
Rademann, J.5
Hilgenfeld, R.6
-
128
-
-
84867091498
-
Impairment of prostate cancer cell growth by a selective and reversible lysine-specific demethylase 1 inhibitor
-
Willmann, D.; Lim, S.; Wetzel, S.; Metzger, E.; Jandausch, A.; Wilk, W.; Jung, M.; Forne, I.; Imhof, A.; Janzer, A.; Kirfel, J.; Waldmann, H.; Schüle, R.; Buettner, R. Impairment of prostate cancer cell growth by a selective and reversible lysine-specific demethylase 1 inhibitor Int. J. Cancer 2012, 131 (11) 2704-2709 10.1002/ijc.27555
-
(2012)
Int. J. Cancer
, vol.131
, Issue.11
, pp. 2704-2709
-
-
Willmann, D.1
Lim, S.2
Wetzel, S.3
Metzger, E.4
Jandausch, A.5
Wilk, W.6
Jung, M.7
Forne, I.8
Imhof, A.9
Janzer, A.10
Kirfel, J.11
Waldmann, H.12
Schüle, R.13
Buettner, R.14
-
129
-
-
77954288774
-
Dali server: Conservation mapping in 3D
-
(Web Server issue)
-
Holm, L.; Rosenström, P. Dali server: conservation mapping in 3D Nucleic Acids Res. 2010, 38 (Suppl. 2) W545-W549 (Web Server issue) 10.1093/nar/gkq366
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. W545-W549
-
-
Holm, L.1
Rosenström, P.2
-
130
-
-
77952362757
-
A scaffold-tree-merging strategy for prospective bioactivity annotation of gamma-pyrones
-
Wetzel, S.; Wilk, W.; Chammaa, S.; Sperl, B.; Roth, A. G.; Yektaoglu, A.; Renner, S.; Berg, T.; Arenz, C.; Giannis, A.; Oprea, T. I.; Rauh, D.; Kaiser, M.; Waldmann, H. A scaffold-tree-merging strategy for prospective bioactivity annotation of gamma-pyrones Angew. Chem., Int. Ed. 2010, 49 (21) 3666-3670 10.1002/anie.200906555
-
(2010)
Angew. Chem., Int. Ed.
, vol.49
, Issue.21
, pp. 3666-3670
-
-
Wetzel, S.1
Wilk, W.2
Chammaa, S.3
Sperl, B.4
Roth, A.G.5
Yektaoglu, A.6
Renner, S.7
Berg, T.8
Arenz, C.9
Giannis, A.10
Oprea, T.I.11
Rauh, D.12
Kaiser, M.13
Waldmann, H.14
-
131
-
-
84969512727
-
-
Resource for Biocomputing, Visualization, and Informatics. Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California (600 16th Street, San Francisco, California 94143-2240, U.S.)
-
UCSF Chimera: A Visualization System for Exploratory Research and Analysis; Resource for Biocomputing, Visualization, and Informatics. Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California (600 16th Street, San Francisco, California 94143-2240, U.S.), 2015.
-
(2015)
UCSF Chimera: A Visualization System for Exploratory Research and Analysis
-
-
-
132
-
-
77951844975
-
Teaching old receptors new tricks: Biasing seven-transmembrane receptors
-
Rajagopal, S.; Rajagopal, K.; Lefkowitz, R. J. Teaching old receptors new tricks: biasing seven-transmembrane receptors Nat. Rev. Drug Discovery 2010, 9 (5) 373-386 10.1038/nrd3024
-
(2010)
Nat. Rev. Drug Discovery
, vol.9
, Issue.5
, pp. 373-386
-
-
Rajagopal, S.1
Rajagopal, K.2
Lefkowitz, R.J.3
-
133
-
-
84887977891
-
Drug repurposing: Translational pharmacology, chemistry, computers and the clinic
-
Issa, N. T.; Byers, S. W.; Dakshanamurthy, S. Drug repurposing: translational pharmacology, chemistry, computers and the clinic Curr. Top. Med. Chem. 2013, 13 (18) 2328-2336 10.2174/15680266113136660163
-
(2013)
Curr. Top. Med. Chem.
, vol.13
, Issue.18
, pp. 2328-2336
-
-
Issa, N.T.1
Byers, S.W.2
Dakshanamurthy, S.3
-
134
-
-
79960809682
-
Old friends in new guise: Repositioning of known drugs with structural bioinformatics
-
Haupt, V. J.; Schroeder, M. Old friends in new guise: repositioning of known drugs with structural bioinformatics Briefings Bioinf. 2011, 12 (4) 312-326 10.1093/bib/bbr011
-
(2011)
Briefings Bioinf.
, vol.12
, Issue.4
, pp. 312-326
-
-
Haupt, V.J.1
Schroeder, M.2
-
135
-
-
84937577473
-
Novel insight into drug repositioning: Methylthiouracil as a case in point
-
Baek, M.-C.; Jung, B.; Kang, H.; Lee, H.-S.; Bae, J.-S. Novel insight into drug repositioning: methylthiouracil as a case in point Pharmacol. Res. 2015, 99, 185-193 10.1016/j.phrs.2015.06.008
-
(2015)
Pharmacol. Res.
, vol.99
, pp. 185-193
-
-
Baek, M.-C.1
Jung, B.2
Kang, H.3
Lee, H.-S.4
Bae, J.-S.5
-
136
-
-
80053512597
-
Open Babel: An open chemical toolbox
-
OBoyle, N. M.; Banck, M.; James, C. A.; Morley, C.; Vandermeersch, T.; Hutchison, G. R. Open Babel: An open chemical toolbox J. Cheminf. 2011, 3 (1) 33 10.1186/1758-2946-3-33
-
(2011)
J. Cheminf.
, vol.3
, Issue.1
, pp. 33
-
-
O'Boyle, N.M.1
Banck, M.2
James, C.A.3
Morley, C.4
Vandermeersch, T.5
Hutchison, G.R.6
-
137
-
-
74049089230
-
-
Rahman, S. A.; Bashton, M.; Holliday, G. L.; Schrader, R.; Thornton, J. M. J. Cheminf. 2009, 1 (1) 12 10.1186/1758-2946-1-12
-
(2009)
J. Cheminf.
, vol.1
, Issue.1
, pp. 12
-
-
Rahman, S.A.1
Bashton, M.2
Holliday, G.L.3
Schrader, R.4
Thornton, J.M.5
-
138
-
-
0035658264
-
BindingDB: A web-accessible molecular recognition database
-
Chen, X.; Liu, M.; Gilson, M. K. BindingDB: a web-accessible molecular recognition database Comb. Chem. High Throughput Screening 2001, 4 (8) 719-725 10.2174/1386207013330670
-
(2001)
Comb. Chem. High Throughput Screening
, vol.4
, Issue.8
, pp. 719-725
-
-
Chen, X.1
Liu, M.2
Gilson, M.K.3
-
139
-
-
84859417074
-
Identification of putative molecular imaging probes for BACE-1 by accounting for protein flexibility in virtual screening
-
Lang, H.; Huang, X.; Yang, Y. Identification of putative molecular imaging probes for BACE-1 by accounting for protein flexibility in virtual screening J. Alzheimers Dis. 2012, 29 (2) 351-359 10.3233/JAD-2011-111787
-
(2012)
J. Alzheimers Dis.
, vol.29
, Issue.2
, pp. 351-359
-
-
Lang, H.1
Huang, X.2
Yang, Y.3
-
140
-
-
84940029055
-
Computational polypharmacology comes of age
-
Rastelli, G.; Pinzi, L. Computational polypharmacology comes of age Front. Pharmacol. 2015, 6, 7874 10.3389/fphar.2015.00157
-
(2015)
Front. Pharmacol.
, vol.6
, pp. 7874
-
-
Rastelli, G.1
Pinzi, L.2
-
141
-
-
84924026602
-
Polypharmacology rescored: Protein-ligand interaction profiles for remote binding site similarity assessment
-
Salentin, S.; Haupt, V. J.; Daminelli, S.; Schroeder, M. Polypharmacology rescored: protein-ligand interaction profiles for remote binding site similarity assessment Prog. Biophys. Mol. Biol. 2014, 116 (2-3) 174-186 10.1016/j.pbiomolbio.2014.05.006
-
(2014)
Prog. Biophys. Mol. Biol.
, vol.116
, Issue.23
, pp. 174-186
-
-
Salentin, S.1
Haupt, V.J.2
Daminelli, S.3
Schroeder, M.4
-
142
-
-
34548827350
-
Nelfinavir, A lead HIV protease inhibitor, is a broad-spectrum, anticancer agent that induces endoplasmic reticulum stress, autophagy, and apoptosis in vitro and in vivo
-
Gills, J. J.; Lopiccolo, J.; Tsurutani, J.; Shoemaker, R. H.; Best, C. J. M.; Abu-Asab, M. S.; Borojerdi, J.; Warfel, N. A.; Gardner, E. R.; Danish, M.; Hollander, M. C.; Kawabata, S.; Tsokos, M.; Figg, W. D.; Steeg, P. S.; Dennis, P. A. Nelfinavir, A lead HIV protease inhibitor, is a broad-spectrum, anticancer agent that induces endoplasmic reticulum stress, autophagy, and apoptosis in vitro and in vivo Clin. Cancer Res. 2007, 13 (17) 5183-5194 10.1158/1078-0432.CCR-07-0161
-
(2007)
Clin. Cancer Res.
, vol.13
, Issue.17
, pp. 5183-5194
-
-
Gills, J.J.1
Lopiccolo, J.2
Tsurutani, J.3
Shoemaker, R.H.4
Best, C.J.M.5
Abu-Asab, M.S.6
Borojerdi, J.7
Warfel, N.A.8
Gardner, E.R.9
Danish, M.10
Hollander, M.C.11
Kawabata, S.12
Tsokos, M.13
Figg, W.D.14
Steeg, P.S.15
Dennis, P.A.16
-
143
-
-
62449113374
-
Old and new pharmacology: Positive allosteric modulation of the alpha7 nicotinic acetylcholine receptor by the 5-hydroxytryptamine(2B/C) receptor antagonist SB-206553 (3,5-dihydro-5-methyl-N-3-pyridinylbenzo[1,2-b:4,5-b′]di pyrrole-1(2H)-carboxamide
-
Dunlop, J.; Lock, T.; Jow, B.; Sitzia, F.; Grauer, S.; Jow, F.; Kramer, A.; Bowlby, M. R.; Randall, A.; Kowal, D.; Gilbert, A.; Comery, T. A.; Larocque, J.; Soloveva, V.; Brown, J.; Roncarati, R. Old and new pharmacology: positive allosteric modulation of the alpha7 nicotinic acetylcholine receptor by the 5-hydroxytryptamine(2B/C) receptor antagonist SB-206553 (3,5-dihydro-5-methyl-N-3-pyridinylbenzo[1,2-b:4,5-b′]di pyrrole-1(2H)-carboxamide J. Pharmacol. Exp. Ther. 2009, 328 (3) 766-776 10.1124/jpet.108.146514
-
(2009)
J. Pharmacol. Exp. Ther.
, vol.328
, Issue.3
, pp. 766-776
-
-
Dunlop, J.1
Lock, T.2
Jow, B.3
Sitzia, F.4
Grauer, S.5
Jow, F.6
Kramer, A.7
Bowlby, M.R.8
Randall, A.9
Kowal, D.10
Gilbert, A.11
Comery, T.A.12
Larocque, J.13
Soloveva, V.14
Brown, J.15
Roncarati, R.16
-
144
-
-
8944239873
-
Potent, selective tetrahydro-beta-carboline antagonists of the serotonin 2B (5HT2B) contractile receptor in the rat stomach fundus
-
Audia, J. E.; Evrard, D. A.; Murdoch, G. R.; Droste, J. J.; Nissen, J. S.; Schenck, K. W.; Fludzinski, P.; Lucaites, V. L.; Nelson, D. L.; Cohen, M. L. Potent, selective tetrahydro-beta-carboline antagonists of the serotonin 2B (5HT2B) contractile receptor in the rat stomach fundus J. Med. Chem. 1996, 39 (14) 2773-2780 10.1021/jm960062t
-
(1996)
J. Med. Chem.
, vol.39
, Issue.14
, pp. 2773-2780
-
-
Audia, J.E.1
Evrard, D.A.2
Murdoch, G.R.3
Droste, J.J.4
Nissen, J.S.5
Schenck, K.W.6
Fludzinski, P.7
Lucaites, V.L.8
Nelson, D.L.9
Cohen, M.L.10
-
145
-
-
84901979488
-
Structural bioinformatics of the interactome
-
Petrey, D.; Honig, B. Structural bioinformatics of the interactome Annu. Rev. Biophys. 2014, 43, 193-210 10.1146/annurev-biophys-051013-022726
-
(2014)
Annu. Rev. Biophys.
, vol.43
, pp. 193-210
-
-
Petrey, D.1
Honig, B.2
-
146
-
-
52249120794
-
An inhibitor of FtsZ with potent and selective anti-staphylococcal activity
-
Haydon, D. J.; Stokes, N. R.; Ure, R.; Galbraith, G.; Bennett, J. M.; Brown, D. R.; Baker, P. J.; Barynin, V. V.; Rice, D. W.; Sedelnikova, S. E.; Heal, J. R.; Sheridan, J. M.; Aiwale, S. T.; Chauhan, P. K.; Srivastava, A.; Taneja, A.; Collins, I.; Errington, J.; Czaplewski, L. G. An inhibitor of FtsZ with potent and selective anti-staphylococcal activity Science 2008, 321 (5896) 1673-1675 10.1126/science.1159961
-
(2008)
Science
, vol.321
, Issue.5896
, pp. 1673-1675
-
-
Haydon, D.J.1
Stokes, N.R.2
Ure, R.3
Galbraith, G.4
Bennett, J.M.5
Brown, D.R.6
Baker, P.J.7
Barynin, V.V.8
Rice, D.W.9
Sedelnikova, S.E.10
Heal, J.R.11
Sheridan, J.M.12
Aiwale, S.T.13
Chauhan, P.K.14
Srivastava, A.15
Taneja, A.16
Collins, I.17
Errington, J.18
Czaplewski, L.G.19
-
147
-
-
84869411678
-
Comparison of small molecule inhibitors of the bacterial cell division protein FtsZ and identification of a reliable cross-species inhibitor
-
Anderson, D. E.; Kim, M. B.; Moore, J. T.; OBrien, T. E.; Sorto, N. A.; Grove, C. I.; Lackner, L. L.; Ames, J. B.; Shaw, J. T. Comparison of small molecule inhibitors of the bacterial cell division protein FtsZ and identification of a reliable cross-species inhibitor ACS Chem. Biol. 2012, 7 (11) 1918-1928 10.1021/cb300340j
-
(2012)
ACS Chem. Biol.
, vol.7
, Issue.11
, pp. 1918-1928
-
-
Anderson, D.E.1
Kim, M.B.2
Moore, J.T.3
O'Brien, T.E.4
Sorto, N.A.5
Grove, C.I.6
Lackner, L.L.7
Ames, J.B.8
Shaw, J.T.9
-
148
-
-
77951984524
-
The antibacterial cell division inhibitor PC190723 is an FtsZ polymer-stabilizing agent that induces filament assembly and condensation
-
Andreu, J. M.; Schaffner-Barbero, C.; Huecas, S.; Alonso, D.; Lopez-Rodriguez, M. L.; Ruiz-Avila, L. B.; Núnez-Ramírez, R.; Llorca, O.; Martín-Galiano, A. J. The antibacterial cell division inhibitor PC190723 is an FtsZ polymer-stabilizing agent that induces filament assembly and condensation J. Biol. Chem. 2010, 285 (19) 14239-14246 10.1074/jbc.M109.094722
-
(2010)
J. Biol. Chem.
, vol.285
, Issue.19
, pp. 14239-14246
-
-
Andreu, J.M.1
Schaffner-Barbero, C.2
Huecas, S.3
Alonso, D.4
Lopez-Rodriguez, M.L.5
Ruiz-Avila, L.B.6
Núnez-Ramírez, R.7
Llorca, O.8
Martín-Galiano, A.J.9
-
149
-
-
84924077519
-
An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles
-
Sudha, G.; Nussinov, R.; Srinivasan, N. An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles Prog. Biophys. Mol. Biol. 2014, 116 (2-3) 141-150 10.1016/j.pbiomolbio.2014.07.004
-
(2014)
Prog. Biophys. Mol. Biol.
, vol.116
, Issue.23
, pp. 141-150
-
-
Sudha, G.1
Nussinov, R.2
Srinivasan, N.3
-
150
-
-
84947269147
-
Computational prediction of protein interfaces: A review of data driven methods
-
Xue, L. C.; Dobbs, D.; Bonvin, A. M.; Honavar, V. Computational prediction of protein interfaces: A review of data driven methods FEBS Lett. 2015, 589 (23) 3516-3526 10.1016/j.febslet.2015.10.003
-
(2015)
FEBS Lett.
, vol.589
, Issue.23
, pp. 3516-3526
-
-
Xue, L.C.1
Dobbs, D.2
Bonvin, A.M.3
Honavar, V.4
-
151
-
-
84870777012
-
ALIX is a Lys63-specific polyubiquitin binding protein that functions in retrovirus budding
-
Dowlatshahi, D. P.; Sandrin, V.; Vivona, S.; Shaler, T. A.; Kaiser, S. E.; Melandri, F.; Sundquist, W. I.; Kopito, R. R. ALIX is a Lys63-specific polyubiquitin binding protein that functions in retrovirus budding Dev. Cell 2012, 23 (6) 1247-1254 10.1016/j.devcel.2012.10.023
-
(2012)
Dev. Cell
, vol.23
, Issue.6
, pp. 1247-1254
-
-
Dowlatshahi, D.P.1
Sandrin, V.2
Vivona, S.3
Shaler, T.A.4
Kaiser, S.E.5
Melandri, F.6
Sundquist, W.I.7
Kopito, R.R.8
-
152
-
-
84878980535
-
The yeast Alix homolog Bro1 functions as a ubiquitin receptor for protein sorting into multivesicular endosomes
-
Pashkova, N.; Gakhar, L.; Winistorfer, S. C.; Sunshine, A. B.; Rich, M.; Dunham, M. J.; Yu, L.; Piper, R. C. The yeast Alix homolog Bro1 functions as a ubiquitin receptor for protein sorting into multivesicular endosomes Dev. Cell 2013, 25 (5) 520-533 10.1016/j.devcel.2013.04.007
-
(2013)
Dev. Cell
, vol.25
, Issue.5
, pp. 520-533
-
-
Pashkova, N.1
Gakhar, L.2
Winistorfer, S.C.3
Sunshine, A.B.4
Rich, M.5
Dunham, M.J.6
Yu, L.7
Piper, R.C.8
-
153
-
-
84896717365
-
Identification of distant drug off-targets by direct superposition of binding pocket surfaces
-
Schumann, M.; Armen, R. S. Identification of distant drug off-targets by direct superposition of binding pocket surfaces PLoS One 2013, 8 (12) e83533 10.1371/journal.pone.0083533
-
(2013)
PLoS One
, vol.8
, Issue.12
, pp. e83533
-
-
Schumann, M.1
Armen, R.S.2
-
154
-
-
33746156959
-
Global mapping of pharmacological space
-
Paolini, G. V.; Shapland, R. H. B.; van Hoorn, W. P.; Mason, J. S.; Hopkins, A. L. Global mapping of pharmacological space Nat. Biotechnol. 2006, 24 (7) 805-815 10.1038/nbt1228
-
(2006)
Nat. Biotechnol.
, vol.24
, Issue.7
, pp. 805-815
-
-
Paolini, G.V.1
Shapland, R.H.B.2
Van Hoorn, W.P.3
Mason, J.S.4
Hopkins, A.L.5
-
155
-
-
69949134994
-
A survey of across-target bioactivity results of small molecules in PubChem
-
Han, L.; Wang, Y.; Bryant, S. H. A survey of across-target bioactivity results of small molecules in PubChem Bioinformatics 2009, 25 (17) 2251-2255 10.1093/bioinformatics/btp380
-
(2009)
Bioinformatics
, vol.25
, Issue.17
, pp. 2251-2255
-
-
Han, L.1
Wang, Y.2
Bryant, S.H.3
-
156
-
-
84906997312
-
Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines
-
LaBute, M. X.; Zhang, X.; Lenderman, J.; Bennion, B. J.; Wong, S. E.; Lightstone, F. C. Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines PLoS One 2014, 9 (9) e106298 10.1371/journal.pone.0106298
-
(2014)
PLoS One
, vol.9
, Issue.9
, pp. e106298
-
-
LaBute, M.X.1
Zhang, X.2
Lenderman, J.3
Bennion, B.J.4
Wong, S.E.5
Lightstone, F.C.6
-
157
-
-
0030925920
-
Pfam: A comprehensive database of protein domain families based on seed alignments
-
Sonnhammer, E. L.; Eddy, S. R.; Durbin, R. Pfam: a comprehensive database of protein domain families based on seed alignments Proteins: Struct., Funct., Genet. 1997, 28 (3) 405-420 10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L
-
(1997)
Proteins: Struct., Funct., Genet.
, vol.28
, Issue.3
, pp. 405-420
-
-
Sonnhammer, E.L.1
Eddy, S.R.2
Durbin, R.3
-
158
-
-
45349108801
-
Functional classification of protein kinase binding sites using Cavbase
-
Kuhn, D.; Weskamp, N.; Hüllermeier, E.; Klebe, G. Functional classification of protein kinase binding sites using Cavbase ChemMedChem 2007, 2 (10) 1432-1447 10.1002/cmdc.200700075
-
(2007)
ChemMedChem
, vol.2
, Issue.10
, pp. 1432-1447
-
-
Kuhn, D.1
Weskamp, N.2
Hüllermeier, E.3
Klebe, G.4
-
159
-
-
34547970336
-
17Beta-oestradiol regulates the expression of Na+/K+-ATPase beta1-subunit, sarcoplasmic reticulum Ca2+-ATPase and carbonic anhydrase IV in H9C2 cells
-
Liu, C.-G.; Xu, K.-Q.; Xu, X.; Huang, J.-J.; Xiao, J.-C.; Zhang, J.-P.; Song, H.-P. 17Beta-oestradiol regulates the expression of Na+/K+-ATPase beta1-subunit, sarcoplasmic reticulum Ca2+-ATPase and carbonic anhydrase iv in H9C2 cells Clin. Exp. Pharmacol. Physiol. 2007, 34 (10) 998-1004 10.1111/j.1440-1681.2007.04675.x
-
(2007)
Clin. Exp. Pharmacol. Physiol.
, vol.34
, Issue.10
, pp. 998-1004
-
-
Liu, C.-G.1
Xu, K.-Q.2
Xu, X.3
Huang, J.-J.4
Xiao, J.-C.5
Zhang, J.-P.6
Song, H.-P.7
-
160
-
-
52549098388
-
Inhibition of a cardiac sarcoplasmic reticulum chloride channel by tamoxifen
-
Beca, S.; Pavlov, E.; Kargacin, M. E.; Aschar-Sobbi, R.; French, R. J.; Kargacin, G. J. Inhibition of a cardiac sarcoplasmic reticulum chloride channel by tamoxifen Pfluegers Arch. 2008, 457 (1) 121-135 10.1007/s00424-008-0510-9
-
(2008)
Pfluegers Arch.
, vol.457
, Issue.1
, pp. 121-135
-
-
Beca, S.1
Pavlov, E.2
Kargacin, M.E.3
Aschar-Sobbi, R.4
French, R.J.5
Kargacin, G.J.6
-
161
-
-
84877823202
-
Scoring functions for prediction of protein-ligand interactions
-
Wang, J.-C.; Lin, J.-H. Scoring functions for prediction of protein-ligand interactions Curr. Pharm. Des. 2013, 19 (12) 2174-2182 10.2174/1381612811319120005
-
(2013)
Curr. Pharm. Des.
, vol.19
, Issue.12
, pp. 2174-2182
-
-
Wang, J.-C.1
Lin, J.-H.2
-
162
-
-
84954206661
-
Proteochemometrics: A tool for modeling the molecular interaction space
-
Kubinyi, H. Müller, G. Methods and Principles in Medicinal Chemistry; Wiley-VCH Verlag GmbH & Co. KGaA: Weinheim, Germany, pp, DOI
-
Wikberg, J. E. S.; Lapinsh, M.; Prusis, P. Proteochemometrics: a tool for modeling the molecular interaction space. In Chemogenomics in Drug Discovery; Kubinyi, H.; Müller, G., Eds.; Methods and Principles in Medicinal Chemistry; Wiley-VCH Verlag GmbH & Co. KGaA: Weinheim, Germany, 2004; pp 289-309, DOI: 10.1002/3527603948.ch10.
-
(2004)
Chemogenomics in Drug Discovery
, pp. 289-309
-
-
Wikberg, J.E.S.1
Lapinsh, M.2
Prusis, P.3
-
163
-
-
2542530042
-
The PDBbind database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures
-
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 (12) 2977-2980 10.1021/jm030580l
-
(2004)
J. Med. Chem.
, vol.47
, Issue.12
, pp. 2977-2980
-
-
Wang, R.1
Fang, X.2
Lu, Y.3
Wang, S.4
-
164
-
-
56549131177
-
The thermodynamics of protein-ligand interaction and solvation: Insights for ligand design
-
Olsson, T. S. G.; Williams, M. A.; Pitt, W. R.; Ladbury, J. E. The thermodynamics of protein-ligand interaction and solvation: insights for ligand design J. Mol. Biol. 2008, 384 (4) 1002-1017 10.1016/j.jmb.2008.09.073
-
(2008)
J. Mol. Biol.
, vol.384
, Issue.4
, pp. 1002-1017
-
-
Olsson, T.S.G.1
Williams, M.A.2
Pitt, W.R.3
Ladbury, J.E.4
-
165
-
-
84862068214
-
Hidden relationship between conserved residues and locally conserved phosphate-binding structures in NAD(P)-binding proteins
-
Wu, C. Y.; Hwa, Y. H.; Chen, Y. C.; Lim, C. Hidden relationship between conserved residues and locally conserved phosphate-binding structures in NAD(P)-binding proteins J. Phys. Chem. B 2012, 116 (19) 5644-5652 10.1021/jp3014332
-
(2012)
J. Phys. Chem. B
, vol.116
, Issue.19
, pp. 5644-5652
-
-
Wu, C.Y.1
Hwa, Y.H.2
Chen, Y.C.3
Lim, C.4
-
166
-
-
84969541098
-
Identification of pockets on protein surface to predict protein-ligand binding sites
-
Roterman-Konieczna, I. Focus on Structural Biology; Springer: Dordrecht, The Netherlands
-
Huang, B. Identification of pockets on protein surface to predict protein-ligand binding sites. In Identification of Ligand Binding Site and Protein-Protein Interaction Area; Roterman-Konieczna, I., Ed.; Focus on Structural Biology; Springer: Dordrecht, The Netherlands, 2013; pp 25-39.
-
(2013)
Identification of Ligand Binding Site and Protein-Protein Interaction Area
, pp. 25-39
-
-
Huang, B.1
-
167
-
-
0028871926
-
Dali: A network tool for protein structure comparison
-
Holm, L.; Sander, C. Dali: a network tool for protein structure comparison Trends Biochem. Sci. 1995, 20 (11) 478-480 10.1016/S0968-0004(00)89105-7
-
(1995)
Trends Biochem. Sci.
, vol.20
, Issue.11
, pp. 478-480
-
-
Holm, L.1
Sander, C.2
-
168
-
-
84867749014
-
Proteins of unknown function in the Protein Data Bank (PDB): An inventory of true uncharacterized proteins and computational tools for their analysis
-
Nadzirin, N.; Firdaus-Raih, M. Proteins of unknown function in the Protein Data Bank (PDB): an inventory of true uncharacterized proteins and computational tools for their analysis Int. J. Mol. Sci. 2012, 13 (10) 12761-12772 10.3390/ijms131012761
-
(2012)
Int. J. Mol. Sci.
, vol.13
, Issue.10
, pp. 12761-12772
-
-
Nadzirin, N.1
Firdaus-Raih, M.2
-
169
-
-
84922366672
-
Template-based prediction of protein function
-
Petrey, D.; Chen, T. S.; Deng, L.; Garzon, J. I.; Hwang, H.; Lasso, G.; Lee, H.; Silkov, A.; Honig, B. Template-based prediction of protein function Curr. Opin. Struct. Biol. 2015, 32, 33-38 10.1016/j.sbi.2015.01.007
-
(2015)
Curr. Opin. Struct. Biol.
, vol.32
, pp. 33-38
-
-
Petrey, D.1
Chen, T.S.2
Deng, L.3
Garzon, J.I.4
Hwang, H.5
Lasso, G.6
Lee, H.7
Silkov, A.8
Honig, B.9
-
170
-
-
17444398048
-
Structure-based identification of a novel NTPase from Methanococcus jannaschii
-
Hwang, K. Y.; Chung, J. H.; Kim, S. H.; Han, Y. S.; Cho, Y. Structure-based identification of a novel NTPase from Methanococcus jannaschii Nat. Struct. Biol. 1999, 6 (7) 691-696 10.1038/10745
-
(1999)
Nat. Struct. Biol.
, vol.6
, Issue.7
, pp. 691-696
-
-
Hwang, K.Y.1
Chung, J.H.2
Kim, S.H.3
Han, Y.S.4
Cho, Y.5
-
171
-
-
84891810215
-
ModBase, a database of annotated comparative protein structure models and associated resources
-
(Database issue)
-
Pieper, U.; Webb, B. M.; Dong, G. Q.; Schneidman-Duhovny, D.; Fan, H.; Kim, S. J.; Khuri, N.; Spill, Y. G.; Weinkam, P.; Hammel, M.; Tainer, J. A.; Nilges, M.; Sali, A. ModBase, a database of annotated comparative protein structure models and associated resources Nucleic Acids Res. 2014, 42 (D1) D336-D346 (Database issue) 10.1093/nar/gkt1144
-
(2014)
Nucleic Acids Res.
, vol.42
, Issue.D1
, pp. D336-D346
-
-
Pieper, U.1
Webb, B.M.2
Dong, G.Q.3
Schneidman-Duhovny, D.4
Fan, H.5
Kim, S.J.6
Khuri, N.7
Spill, Y.G.8
Weinkam, P.9
Hammel, M.10
Tainer, J.A.11
Nilges, M.12
Sali, A.13
-
172
-
-
80051512894
-
Expression, purification and preliminary crystallographic analysis of O-acetylhomoserine sulfhydrylase from Mycobacterium tuberculosis
-
Yin, J.; Garen, C. R.; Bateman, K.; Yu, M.; Lyon, E. Z. A.; Habel, J.; Kim, H.; Hung, L.-w.; Kim, C.-Y.; James, M. N. G. Expression, purification and preliminary crystallographic analysis of O-acetylhomoserine sulfhydrylase from Mycobacterium tuberculosis Acta Crystallogr., Sect. F: Struct. Biol. Cryst. Commun. 2011, 67 (Part 8) 959-963 10.1107/S1744309111017611
-
(2011)
Acta Crystallogr., Sect. F: Struct. Biol. Cryst. Commun.
, vol.67
, pp. 959-963
-
-
Yin, J.1
Garen, C.R.2
Bateman, K.3
Yu, M.4
Lyon, E.Z.A.5
Habel, J.6
Kim, H.7
Hung, L.-W.8
Kim, C.-Y.9
James, M.N.G.10
-
173
-
-
39449115394
-
I-TASSER server for protein 3D structure prediction
-
Zhang, Y. I-TASSER server for protein 3D structure prediction BMC Bioinf. 2008, 9, 40 10.1186/1471-2105-9-40
-
(2008)
BMC Bioinf.
, vol.9
, pp. 40
-
-
Zhang, Y.1
-
174
-
-
84874093356
-
The state of the human proteome in 2012 as viewed through PeptideAtlas
-
Farrah, T.; Deutsch, E. W.; Hoopmann, M. R.; Hallows, J. L.; Sun, Z.; Huang, C.-Y.; Moritz, R. L. The state of the human proteome in 2012 as viewed through PeptideAtlas J. Proteome Res. 2013, 12 (1) 162-171 10.1021/pr301012j
-
(2013)
J. Proteome Res.
, vol.12
, Issue.1
, pp. 162-171
-
-
Farrah, T.1
Deutsch, E.W.2
Hoopmann, M.R.3
Hallows, J.L.4
Sun, Z.5
Huang, C.-Y.6
Moritz, R.L.7
-
175
-
-
59849127275
-
The origin, evolution and structure of the protein world
-
Caetano-Anollés, G.; Wang, M.; Caetano-Anollés, D.; Mittenthal, J. E. The origin, evolution and structure of the protein world Biochem. J. 2009, 417 (3) 621-637 10.1042/BJ20082063
-
(2009)
Biochem. J.
, vol.417
, Issue.3
, pp. 621-637
-
-
Caetano-Anollés, G.1
Wang, M.2
Caetano-Anollés, D.3
Mittenthal, J.E.4
-
176
-
-
0037030707
-
Structural classification of protein kinases using 3D molecular interaction field analysis of their ligand binding sites: Target family landscapes
-
Naumann, T.; Matter, H. Structural classification of protein kinases using 3D molecular interaction field analysis of their ligand binding sites: target family landscapes J. Med. Chem. 2002, 45 (12) 2366-2378 10.1021/jm011002c
-
(2002)
J. Med. Chem.
, vol.45
, Issue.12
, pp. 2366-2378
-
-
Naumann, T.1
Matter, H.2
-
177
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S. F.; Madden, T. L.; Schäffer, A. A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 1997, 25 (17) 3389-3402 10.1093/nar/25.17.3389
-
(1997)
Nucleic Acids Res.
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
178
-
-
0025882349
-
PROSITE: A dictionary of sites and patterns in proteins
-
Bairoch, A. PROSITE: a dictionary of sites and patterns in proteins Nucleic Acids Res. 1991, 19 (Suppl) 2241-2245 10.1093/nar/19.suppl.2241
-
(1991)
Nucleic Acids Res.
, vol.19
, pp. 2241-2245
-
-
Bairoch, A.1
-
179
-
-
84907398358
-
Simple Ligand-Receptor Interaction Descriptor (SILIRID) for alignment-free binding site comparison
-
Chupakhin, V.; Marcou, G.; Gaspar, H.; Varnek, A. Simple Ligand-Receptor Interaction Descriptor (SILIRID) for alignment-free binding site comparison Comput. Struct. Biotechnol. J. 2014, 10 (16) 33-37 10.1016/j.csbj.2014.05.004
-
(2014)
Comput. Struct. Biotechnol. J.
, vol.10
, Issue.16
, pp. 33-37
-
-
Chupakhin, V.1
Marcou, G.2
Gaspar, H.3
Varnek, A.4
-
180
-
-
84940205919
-
Detection of binding site molecular interaction field similarities
-
Chartier, M.; Najmanovich, R. Detection of binding site molecular interaction field similarities J. Chem. Inf. Model. 2015, 55 (8) 1600-1615 10.1021/acs.jcim.5b00333
-
(2015)
J. Chem. Inf. Model.
, vol.55
, Issue.8
, pp. 1600-1615
-
-
Chartier, M.1
Najmanovich, R.2
-
181
-
-
38149096341
-
Similarity search for local protein structures at atomic resolution by exploiting a database management system
-
Kinjo, A. R.; Nakamura, H. Similarity search for local protein structures at atomic resolution by exploiting a database management system Biophysics 2007, 3, 75-84 10.2142/biophysics.3.75
-
(2007)
Biophysics
, vol.3
, pp. 75-84
-
-
Kinjo, A.R.1
Nakamura, H.2
-
182
-
-
59649095965
-
Comprehensive structural classification of ligand-binding motifs in proteins
-
Kinjo, A. R.; Nakamura, H. Comprehensive structural classification of ligand-binding motifs in proteins Structure 2009, 17 (2) 234-246 10.1016/j.str.2008.11.009
-
(2009)
Structure
, vol.17
, Issue.2
, pp. 234-246
-
-
Kinjo, A.R.1
Nakamura, H.2
-
183
-
-
23444459516
-
Connecting the protein structure universe by using sparse recurring fragments
-
Friedberg, I.; Godzik, A. Connecting the protein structure universe by using sparse recurring fragments Structure 2005, 13 (8) 1213-1224 10.1016/j.str.2005.05.009
-
(2005)
Structure
, vol.13
, Issue.8
, pp. 1213-1224
-
-
Friedberg, I.1
Godzik, A.2
-
184
-
-
84887460366
-
An aggregate analysis of many predicted structures to reduce errors in protein structure comparison caused by conformational flexibility
-
Godshall, B. G.; Tang, Y.; Yang, W.; Chen, B. Y. An aggregate analysis of many predicted structures to reduce errors in protein structure comparison caused by conformational flexibility BMC Struct. Biol. 2013, 13 (Suppl. 1) S10 10.1186/1472-6807-13-S1-S10
-
(2013)
BMC Struct. Biol.
, vol.13
, pp. S10
-
-
Godshall, B.G.1
Tang, Y.2
Yang, W.3
Chen, B.Y.4
-
185
-
-
84895469259
-
Exploiting structural information for drug-target assessment
-
Volkamer, A.; Rarey, M. Exploiting structural information for drug-target assessment Future Med. Chem. 2014, 6 (3) 319-331 10.4155/fmc.14.3
-
(2014)
Future Med. Chem.
, vol.6
, Issue.3
, pp. 319-331
-
-
Volkamer, A.1
Rarey, M.2
|