-
1
-
-
54249155522
-
Network pharmacology: The next paradigm in drug discovery
-
Hopkins AL. Network pharmacology: the next paradigm in drug discovery. Nat. Chem. Biol. 4(11), 682-690 (2008).
-
(2008)
Nat. Chem. Biol.
, vol.4
, Issue.11
, pp. 682-690
-
-
Hopkins, A.L.1
-
2
-
-
59349083179
-
Mechanisms of drug combinations: Interaction and network perspectives
-
Jia J, Zhu F, Ma X, Cao ZW, Li YX, Chen YZ. Mechanisms of drug combinations: interaction and network perspectives. Nat. Rev. Drug Discov. 8(2), 111-128 (2009).
-
(2009)
Nat. Rev. Drug Discov.
, vol.8
, Issue.2
, pp. 111-128
-
-
Jia, J.1
Zhu, F.2
Ma, X.3
Cao, Z.W.4
Li, Y.X.5
Chen, Y.Z.6
-
3
-
-
84891743052
-
Promiscuous drugs: Superior efficacy of one pill on many targets
-
Miller MD. Promiscuous drugs: superior efficacy of one pill on many targets. Ab. Papers Am. Chem. Soc. 229, U157-U157 (2005).
-
(2005)
Ab. Papers Am. Chem. Soc.
, vol.229
-
-
Miller, M.D.1
-
4
-
-
51349085387
-
Data completeness - The Achilles heel of drug-target networks
-
Mestres J, Gregori-Puigjane E, Valverde S, Sole RV. Data completeness - the Achilles heel of drug-target networks. Nat. Biotechnol. 26(9), 983-984 (2008).
-
(2008)
Nat. Biotechnol.
, vol.26
, Issue.9
, pp. 983-984
-
-
Mestres, J.1
Gregori-Puigjane, E.2
Valverde, S.3
Sole, R.V.4
-
5
-
-
33746156959
-
Global mapping of pharmacological space
-
Paolini GV, Shapland RHB, van Hoorn WP, Mason JS, Hopkins AL. Global mapping of pharmacological space. Nat. Biotechnol. 24(7), 805-815 (2006).
-
(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
-
6
-
-
70449634957
-
Predicting new molecular targets for known drugs
-
Keiser MJ, Setola V, Irwin JJ et al. Predicting new molecular targets for known drugs. Nature 462, 175-181 (2009).
-
(2009)
Nature
, vol.462
, pp. 175-181
-
-
Keiser, M.J.1
Setola, V.2
Irwin, J.J.3
-
7
-
-
45349108801
-
Functional classification of protein kinase binding sites using CavBase
-
Kuhn D, Weskamp N, Hullermeier E, Klebe G. Functional classification of protein kinase binding sites using CavBase. ChemMedChem 2(10), 1432-1447 (2007).
-
(2007)
ChemMedChem
, vol.2
, Issue.10
, pp. 1432-1447
-
-
Kuhn, D.1
Weskamp, N.2
Hullermeier, E.3
Klebe, G.4
-
8
-
-
33644646963
-
Classification and comparison of ligand-binding sites derived from grid-mapped knowledge-based potentials
-
Hoppe C, Steinbeck C, Wohfahrt G. Classification and comparison of ligand-binding sites derived from grid-mapped knowledge-based potentials. J. Mol. Graph. Model. 24(5), 328-340 (2006).
-
(2006)
J. Mol. Graph. Model.
, vol.24
, Issue.5
, pp. 328-340
-
-
Hoppe, C.1
Steinbeck, C.2
Wohfahrt, G.3
-
9
-
-
26944452838
-
Structure-based approaches to improve selectivity: CDK2-GSK3 beta binding site analysis
-
Vulpetti A, Crivori P, Cameron A et al. Structure-based approaches to improve selectivity: CDK2-GSK3 beta binding site analysis. J. Chem. Inf. Model. 45(5), 1282-1290 (2005).
-
(2005)
J. Chem. Inf. Model.
, vol.45
, Issue.5
, pp. 1282-1290
-
-
Vulpetti, A.1
Crivori, P.2
Cameron, A.3
-
12
-
-
17144373303
-
Druggability indices for protein targets derived from NMR-based screening data
-
Hajduk PJ, Huth JR, Fesik SW. Druggability indices for protein targets derived from NMR-based screening data. J. Med. Chem. 48(7), 2518-2525 (2005).
-
(2005)
J. Med. Chem.
, vol.48
, Issue.7
, pp. 2518-2525
-
-
Hajduk, P.J.1
Huth, J.R.2
Fesik, S.W.3
-
13
-
-
79953703975
-
Fragment screening to predict druggability (ligandability) and lead discovery success
-
Edfeldt FNB, Folmer RHA, Breeze AL. Fragment screening to predict druggability (ligandability) and lead discovery success. Drug Discov. Today 16(7-8), 284-287 (2011).
-
(2011)
Drug Discov. Today
, vol.16
, Issue.7-8
, pp. 284-287
-
-
Edfeldt, F.N.B.1
Folmer, R.H.A.2
Breeze, A.L.3
-
14
-
-
36049036606
-
19F-NMR screening: Principles and applications to drug discovery
-
19F-NMR screening: principles and applications to drug discovery. Prog. Nuclear Mag. Reson. Spect. 51(4), 243-24I (2007).
-
(2007)
Prog. Nuclear Mag. Reson. Spect.
, vol.51
, Issue.4
-
-
Dalvit, C.1
-
15
-
-
70349124638
-
Design and NMR-based screening of LEF, a library of chemical fragments with different local environment of fluorine
-
Vulpetti A, Hommel U, Landrum G, Lewis R, Dalvit C. Design and NMR-based screening of LEF, a library of chemical fragments with different local environment of fluorine. J. Am. Chem. Soc. 131(36), 12949-12959 (2009).
-
(2009)
J. Am. Chem. Soc.
, vol.131
, Issue.36
, pp. 12949-12959
-
-
Vulpetti, A.1
Hommel, U.2
Landrum, G.3
Lewis, R.4
Dalvit, C.5
-
17
-
-
67649422714
-
Fpocket: An open source platform for ligand pocket detection
-
Le Guilloux V, Schmidtke P, Tuffery P. Fpocket: an open source platform for ligand pocket detection. BMC Bioinform. 10, 168 (2009).
-
(2009)
BMC Bioinform.
, vol.10
, pp. 168
-
-
Le Guilloux, V.1
Schmidtke, P.2
Tuffery, P.3
-
18
-
-
0342424187
-
Fast prediction and visualization of protein binding pockets with PASS
-
Brady GP, Stouten PFW. Fast prediction and visualization of protein binding pockets with PASS. J. Comput. Aided Mol. Des. 14(4), 383-401 (2000).
-
(2000)
J. Comput. Aided Mol. Des.
, vol.14
, Issue.4
, pp. 383-401
-
-
Brady, G.P.1
Stouten, P.F.W.2
-
19
-
-
33750029942
-
LIGSITE(csc): Predicting ligand binding sites using the Connolly surface and degree of conservation
-
Huang BD, Schroeder M. LIGSITE(csc): predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct. Biol. 6, 19 (2006).
-
(2006)
BMC Struct. Biol.
, vol.6
, pp. 19
-
-
Huang, B.D.1
Schroeder, M.2
-
20
-
-
21044444449
-
Pocketome via comprehensive identification and classification of ligand binding envelopes
-
An JH, Totrov M, Abagyan R. Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol. Cell. Proteo. 4(6), 752-761 (2005).
-
(2005)
Mol. Cell. Proteo.
, vol.4
, Issue.6
, pp. 752-761
-
-
An, J.H.1
Totrov, M.2
Abagyan, R.3
-
21
-
-
34547341277
-
PocketPicker: Analysis of ligand binding-sites with shape descriptors
-
Weisel M, Proschak E, Schneider G. PocketPicker: analysis of ligand binding-sites with shape descriptors. Chem. Central J. 1, 7 (2007).
-
(2007)
Chem. Central J.
, vol.1
, pp. 7
-
-
Weisel, M.1
Proschak, E.2
Schneider, G.3
-
22
-
-
79551593452
-
MSPocket: An orientation-independent algorithm for the detection of ligand binding pockets
-
Zhu HB, Pisabarro MT. MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets. Bioinformatics 27(3), 351-358 (2011).
-
(2011)
Bioinformatics
, vol.27
, Issue.3
, pp. 351-358
-
-
Zhu, H.B.1
Pisabarro, M.T.2
-
23
-
-
77955517509
-
Druggable pockets and binding site centric chemical space: A paradigm shift in drug discovery
-
Perot S, Sperandio O, Miteva MA, Camproux AC, Villoutreix BO. Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery. Drug Discov. Today 15(15-16), 656-667 (2010).
-
(2010)
Drug Discov. Today
, vol.15
, Issue.15-16
, pp. 656-667
-
-
Perot, S.1
Sperandio, O.2
Miteva, M.A.3
Camproux, A.C.4
Villoutreix, B.O.5
-
24
-
-
77953504480
-
In silico prediction of binding sites on proteins
-
Leis S, Schneider S, Zacharias M. In silico prediction of binding sites on proteins. Curr. Med. Chem. 17(15), 1550-1562 (2010).
-
(2010)
Curr. Med. Chem.
, vol.17
, Issue.15
, pp. 1550-1562
-
-
Leis, S.1
Schneider, S.2
Zacharias, M.3
-
25
-
-
78650714726
-
Large-scale comparison of four binding site detection algorithms
-
Schmidtke P, Souaille C, Estienne F, Baurin N, Kroemer RT. Large-scale comparison of four binding site detection algorithms. J. Chem. Inf. Model. 50(12), 2191-2200 (2010).
-
(2010)
J. Chem. Inf. Model.
, vol.50
, Issue.12
, pp. 2191-2200
-
-
Schmidtke, P.1
Souaille, C.2
Estienne, F.3
Baurin, N.4
Kroemer, R.T.5
-
26
-
-
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. 4(3), 209-220 (2008).
-
(2008)
Curr. Comput. Aided Drug Des.
, vol.4
, Issue.3
, pp. 209-220
-
-
Kellenberger, E.1
Schalon, C.2
Rognan, D.3
-
27
-
-
76649139794
-
Computational approaches to identifying and characterizing protein binding sites for ligand design
-
Henrich S, Salo-Ahen OMH, Huang B, Rippmann F, Cruciani G, Wade RC. Computational approaches to identifying and characterizing protein binding sites for ligand design. J. Mol. Recog. 23(2), 209-219 (2010).
-
(2010)
J. Mol. Recog.
, vol.23
, Issue.2
, pp. 209-219
-
-
Henrich, S.1
Salo-Ahen, O.M.H.2
Huang, B.3
Rippmann, F.4
Cruciani, G.5
Wade, R.C.6
-
28
-
-
84860838201
-
Structure-based computational analysis of protein binding sites for function and druggability prediction
-
Nisius B, Sha F, Gohlke H. Structure-based computational analysis of protein binding sites for function and druggability prediction. J. Biotechnol. 159(3), 123-134 (2012).
-
(2012)
J. Biotechnol.
, vol.159
, Issue.3
, pp. 123-134
-
-
Nisius, B.1
Sha, F.2
Gohlke, H.3
-
29
-
-
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. 323(2), 387-406 (2002).
-
(2002)
J. Mol. Biol.
, vol.323
, Issue.2
, pp. 387-406
-
-
Schmitt, S.1
Kuhn, D.2
Klebe, G.3
-
30
-
-
33744935012
-
From the similarity analysis of protein cavities to the functional classification of protein families using CavBase
-
Kuhn D, Weskamp N, Schmitt S, Hullermeier E, Klebe G. From the similarity analysis of protein cavities to the functional classification of protein families using CavBase. J. Mol. Biol. 359(4), 1023-1044 (2006).
-
(2006)
J. Mol. Biol.
, vol.359
, Issue.4
, pp. 1023-1044
-
-
Kuhn, D.1
Weskamp, N.2
Schmitt, S.3
Hullermeier, E.4
Klebe, G.5
-
31
-
-
2442614144
-
Recognition of functional sites in protein structures
-
Shulman-Peleg A, Nussinov R, Wolfson HJ. Recognition of functional sites in protein structures. J. Mol. Biol. 339(3), 607-633 (2004).
-
(2004)
J. Mol. Biol.
, vol.339
, Issue.3
, pp. 607-633
-
-
Shulman-Peleg, A.1
Nussinov, R.2
Wolfson, H.J.3
-
32
-
-
23144456254
-
SiteEngines: Recognition and comparison of binding sites and protein-protein interfaces
-
Shulman-Peleg A, Nussinov R, Wolfson HJ. SiteEngines: recognition and comparison of binding sites and protein-protein interfaces. Nucleic Acids Res. 33, W337-W341 (2005).
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Shulman-Peleg, A.1
Nussinov, R.2
Wolfson, H.J.3
-
33
-
-
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. Prot. Struct. Funct. Gene. 52(2), 137-145 (2003).
-
(2003)
Prot. Struct. Funct. Gene.
, vol.52
, Issue.2
, pp. 137-145
-
-
Jambon, M.1
Imberty, A.2
Deleage, G.3
Geourjon, C.4
-
34
-
-
44449139387
-
Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments
-
Xie L, Bourne PE. Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc. Natl Acad. Sci. USA 105(14), 5441-5446 (2008).
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, Issue.14
, pp. 5441-5446
-
-
Xie, L.1
Bourne, P.E.2
-
35
-
-
33644876699
-
SitesBase: A database for structure-based protein-ligand binding site comparisons
-
Gold ND, Jackson RM. SitesBase: a database for structure-based protein-ligand binding site comparisons. Nucleic Acids Res. 34, D231-D234 (2006).
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Gold, N.D.1
Jackson, R.M.2
-
36
-
-
66349094968
-
Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation
-
Wallach I, Lilien RH. Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation. Bioinformatics 25(12), I296-I304 (2009).
-
(2009)
Bioinformatics
, vol.25
, Issue.12
-
-
Wallach, I.1
Lilien, R.H.2
-
37
-
-
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 JS. A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for ligands and proteins (FLAP): theory and application. J. Chem. Inf. Model. 47(2), 279-294 (2007).
-
(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
-
38
-
-
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. 50(1), 123-135 (2010).
-
(2010)
J. Chem. Inf. Model.
, vol.50
, Issue.1
, pp. 123-135
-
-
Weill, N.1
Rognan, D.2
-
39
-
-
77956040404
-
Predicting polypharmacology by binding site similarity: From kinases to the protein universe
-
Milletti F, Vulpetti A. predicting polypharmacology by binding site similarity: from kinases to the protein universe. J. Chem. Inf. Model. 50(8), 1418-1431 (2010).
-
(2010)
J. Chem. Inf. Model.
, vol.50
, Issue.8
, pp. 1418-1431
-
-
Milletti, F.1
Vulpetti, A.2
-
40
-
-
84862181488
-
PoSSuM: A database of similar protein-ligand binding and putative pockets
-
Ito JI, Tabei Y, Shimizu K, Tsuda K, Tomii K. PoSSuM: a database of similar protein-ligand binding and putative pockets. Nucleic Acids Res. 40(D1), D541-D548 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
, Issue.D1
-
-
Ito, J.I.1
Tabei, Y.2
Shimizu, K.3
Tsuda, K.4
Tomii, K.5
-
41
-
-
78349294513
-
Combined use of computational chemistry, NMR screening, and x-ray crystallography for identification and characterization of fluorophilic protein environments
-
Vulpetti A, Schiering N, Dalvit C. Combined use of computational chemistry, NMR screening, and x-ray crystallography for identification and characterization of fluorophilic protein environments. Prot. Struct. Funct. Bioinform. 78(16), 3281-3291 (2010).
-
(2010)
Prot. Struct. Funct. Bioinform.
, vol.78
, Issue.16
, pp. 3281-3291
-
-
Vulpetti, A.1
Schiering, N.2
Dalvit, C.3
-
42
-
-
83455163826
-
Large-scale evaluation of CavBase for analyzing the polypharmacology of kinase inhibitors
-
Kalliokoski T, Vulpetti A. Large-scale evaluation of CavBase for analyzing the polypharmacology of kinase inhibitors. Mol. Inform. 30(11-12), 923-925 (2011).
-
(2011)
Mol. Inform.
, vol.30
, Issue.11-12
, pp. 923-925
-
-
Kalliokoski, T.1
Vulpetti, A.2
-
43
-
-
38049018155
-
A quantitative analysis of kinase inhibitor selectivity
-
Karaman MW, Herrgard S, Treiber DK et al. A quantitative analysis of kinase inhibitor selectivity. Nat. Biotechnol. 26(1), 127-132 (2008).
-
(2008)
Nat. Biotechnol.
, vol.26
, Issue.1
, pp. 127-132
-
-
Karaman, M.W.1
Herrgard, S.2
Treiber, D.K.3
-
44
-
-
65249170904
-
Binding site similarity analysis for the functional classification of the protein kinase family
-
Kinnings SL, Jackson RM. Binding site similarity analysis for the functional classification of the protein kinase family. J. Chem. Inf. Model. 49(2), 318-329 (2009).
-
(2009)
J. Chem. Inf. Model.
, vol.49
, Issue.2
, pp. 318-329
-
-
Kinnings, S.L.1
Jackson, R.M.2
-
45
-
-
45349108801
-
Functional classification of protein kinase binding sites using CavBase
-
Kuhn D, Weskamp N, Hullermeier E, Klebe G. Functional classification of protein kinase binding sites using CavBase. ChemMedChem 2(10), 1432-1447 (2007).
-
(2007)
ChemMedChem
, vol.2
, Issue.10
, pp. 1432-1447
-
-
Kuhn, D.1
Weskamp, N.2
Hullermeier, E.3
Klebe, G.4
-
46
-
-
33947420139
-
Shape variation in protein binding pockets and their ligands
-
Kahraman A, Morris RJ, Laskowski RA, Thornton JM. Shape variation in protein binding pockets and their ligands. J. Mol. Biol. 368(1), 283-301 (2007).
-
(2007)
J. Mol. Biol.
, vol.368
, Issue.1
, pp. 283-301
-
-
Kahraman, A.1
Morris, R.J.2
Laskowski, R.A.3
Thornton, J.M.4
-
47
-
-
77950423796
-
A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: Application to ligand prediction
-
Hoffmann B, Zaslavskiy M, Vert JP, Stoven V. A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction. BMC Bioinform. 11, 99 (2010).
-
(2010)
BMC Bioinform.
, vol.11
, pp. 99
-
-
Hoffmann, B.1
Zaslavskiy, M.2
Vert, J.P.3
Stoven, V.4
-
48
-
-
84855711573
-
Cofactor-binding sites in proteins of deviating sequence: Comparative analysis and clustering in torsion angle, cavity, and fold space
-
Stegemann B, Klebe G. Cofactor-binding sites in proteins of deviating sequence: comparative analysis and clustering in torsion angle, cavity, and fold space. Prot. Struct. Funct. Bioinform. 80(2), 626-648 (2012).
-
(2012)
Prot. Struct. Funct. Bioinform.
, vol.80
, Issue.2
, pp. 626-648
-
-
Stegemann, B.1
Klebe, G.2
-
49
-
-
65249117514
-
Identifying and characterizing binding sites and assessing druggability
-
Halgren TA. Identifying and characterizing binding sites and assessing druggability. J. Chem. Inf. Model. 49(2), 377-389 (2009).
-
(2009)
J. Chem. Inf. Model.
, vol.49
, Issue.2
, pp. 377-389
-
-
Halgren, T.A.1
-
50
-
-
33646757492
-
On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites
-
Nayal M, Honig B. On the nature of cavities on protein surfaces: application to the identification of drug-binding sites. Prot. Struct. Funct. Bioinform. 63(4), 892-906 (2006).
-
(2006)
Prot. Struct. Funct. Bioinform.
, vol.63
, Issue.4
, pp. 892-906
-
-
Nayal, M.1
Honig, B.2
-
51
-
-
82355186340
-
DrugPred: A structure-based approach to predict protein druggability developed using an extensive nonredundant data set
-
Krasowski A, Muthas D, Sarkar A, Schmitt S, Brenk R. DrugPred: a structure-based approach to predict protein druggability developed using an extensive nonredundant data set. J. Chem. Inf. Model. 51(11), 2829-2842 (2011).
-
(2011)
J. Chem. Inf. Model.
, vol.51
, Issue.11
, pp. 2829-2842
-
-
Krasowski, A.1
Muthas, D.2
Sarkar, A.3
Schmitt, S.4
Brenk, R.5
-
52
-
-
78649499434
-
Analyzing the topology of active sites: On the prediction of pockets and subpockets
-
Volkamer A, Griewel A, Grombacher T, Rarey M. Analyzing the topology of active sites: on the prediction of pockets and subpockets. J. Chem. Inf. Model. 50(11), 2041-2052 (2010).
-
(2010)
J. Chem. Inf. Model.
, vol.50
, Issue.11
, pp. 2041-2052
-
-
Volkamer, A.1
Griewel, A.2
Grombacher, T.3
Rarey, M.4
-
53
-
-
77955397914
-
Understanding and predicting druggability. A high-throughput method for detection of drug binding sites
-
Schmidtke P, Barril X. Understanding and predicting druggability. A high-throughput method for detection of drug binding sites. J. Med. Chem. 53(15), 5858-5867 (2010).
-
(2010)
J. Med. Chem.
, vol.53
, Issue.15
, pp. 5858-5867
-
-
Schmidtke, P.1
Barril, X.2
-
54
-
-
84891736667
-
Challenges and strategies in the design of multi-targeted ligands
-
Rankovic Z, Morphy R. Challenges and strategies in the design of multi-targeted ligands. Abstra. Pap. Am. Chem. Soc. 239 (2010).
-
(2010)
Abstra. Pap. Am. Chem. Soc.
, vol.239
-
-
Rankovic, Z.1
Morphy, R.2
-
55
-
-
77649204688
-
Selectively nonselective kinase inhibition: Striking the right balance
-
Morphy R. Selectively nonselective kinase inhibition: striking the right balance. J. Med. Chem. 53(4), 1413-1437 (2010).
-
(2010)
J. Med. Chem.
, vol.53
, Issue.4
, pp. 1413-1437
-
-
Morphy, R.1
-
56
-
-
79959810247
-
Computational tools for polypharmacology and repurposing
-
Achenbach J, Tiikkainen P, Franke L, Proschak E. Computational tools for polypharmacology and repurposing. Future Med. Chem. 3(8), 961-968 (2011).
-
(2011)
Future Med. Chem.
, vol.3
, Issue.8
, pp. 961-968
-
-
Achenbach, J.1
Tiikkainen, P.2
Franke, L.3
Proschak, E.4
-
57
-
-
84859179582
-
Functional prediction of binding pockets
-
Kontoyianni M, Rosnick CB. Functional prediction of binding pockets. J. Chem. Inf. Model. 52(3), 824-833 (2012).
-
(2012)
J. Chem. Inf. Model.
, vol.52
, Issue.3
, pp. 824-833
-
-
Kontoyianni, M.1
Rosnick, C.B.2
-
58
-
-
78649523910
-
Drug-like density: A method of quantifying the 'bindability' of a protein target based on a very large set of pockets and drug-like ligands from the Protein Data Bank
-
Sheridan RP, Maiorov VN, Holloway MK, Cornell WD, Gao YD. Drug-like density: a method of quantifying the 'bindability' of a protein target based on a very large set of pockets and drug-like ligands from the Protein Data Bank. J. Chem. Inf. Model. 50(11), 2029-2040 (2010).
-
(2010)
J. Chem. Inf. Model.
, vol.50
, Issue.11
, pp. 2029-2040
-
-
Sheridan, R.P.1
Maiorov, V.N.2
Holloway, M.K.3
Cornell, W.D.4
Gao, Y.D.5
-
59
-
-
24344487344
-
Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions
-
Mintz S, Shulman-Peleg A, Wolfson HJ, Nussinov R. Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions. Prot. Struct. Funct. Bioinform. 61(1), 6-20 (2005).
-
(2005)
Prot. Struct. Funct. Bioinform.
, vol.61
, Issue.1
, pp. 6-20
-
-
Mintz, S.1
Shulman-Peleg, A.2
Wolfson, H.J.3
Nussinov, R.4
-
60
-
-
80052411919
-
Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM
-
Tuncbag N, Gursoy A, Nussinov R, Keskin O. Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat. Protocols 6 (9), 1341-1354 (2011).
-
(2011)
Nat. Protocols
, vol.6
, Issue.9
, pp. 1341-1354
-
-
Tuncbag, N.1
Gursoy, A.2
Nussinov, R.3
Keskin, O.4
-
61
-
-
31344462177
-
Conformational diversity of ligands bound to proteins
-
Stockwell GR, Thornton JM. Conformational diversity of ligands bound to proteins. J. Mol. Biol. 356(4), 928-944 (2006).
-
(2006)
J. Mol. Biol.
, vol.356
, Issue.4
, pp. 928-944
-
-
Stockwell, G.R.1
Thornton, J.M.2
-
62
-
-
33847659183
-
C-Src binds to the cancer drug imatinib with an inactive Abl/c-Kit conformation and a distributed thermodynamic penalty
-
Seeliger MA, Nagar B, Frank F, Cao X, Henderson MN, Kuriyan J. c-Src binds to the cancer drug imatinib with an inactive Abl/c-Kit conformation and a distributed thermodynamic penalty. Structure 15(3), 299-311 (2007).
-
(2007)
Structure
, vol.15
, Issue.3
, pp. 299-311
-
-
Seeliger, M.A.1
Nagar, B.2
Frank, F.3
Cao, X.4
Henderson, M.N.5
Kuriyan, J.6
-
63
-
-
33646755174
-
A Src-like inactive conformation in the Abl tyrosine kinase domain
-
Levinson NM, Kuchment O, Shen K et al. A Src-like inactive conformation in the Abl tyrosine kinase domain. PloS Biol. 4(5), 753-767 (2006).
-
(2006)
PloS Biol.
, vol.4
, Issue.5
, pp. 753-767
-
-
Levinson, N.M.1
Kuchment, O.2
Shen, K.3
-
64
-
-
0036682301
-
Crystal structures of the kinase domain of c-Abl in complex with the small molecule inhibitors PD173955 and imatinib (STI-571)
-
Nagar B, Bornmann WG, Pellicena P et al. Crystal structures of the kinase domain of c-Abl in complex with the small molecule inhibitors PD173955 and imatinib (STI-571). Cancer Res. 62(15), 4236-4243 (2002).
-
(2002)
Cancer Res.
, vol.62
, Issue.15
, pp. 4236-4243
-
-
Nagar, B.1
Bornmann, W.G.2
Pellicena, P.3
-
65
-
-
33847659183
-
C-Src binds to the cancer drug imatinib with an inactive Abl/c-Kit conformation and a distributed thermodynamic penalty
-
Seeliger MA, Nagar B, Frank F, Cao X, Henderson MN, Kuriyan J. c-Src binds to the cancer drug imatinib with an inactive Abl/c-Kit conformation and a distributed thermodynamic penalty. Structure 15(3), 299-311 (2007).
-
(2007)
Structure
, vol.15
, Issue.3
, pp. 299-311
-
-
Seeliger, M.A.1
Nagar, B.2
Frank, F.3
Cao, X.4
Henderson, M.N.5
Kuriyan, J.6
-
66
-
-
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 et al. Unexpected nanomolar inhibition of carbonic anhydrase by COX-2-selective celecoxib: new pharmacological opportunities due to related binding site recognition. J. Med. Chem. 47(3), 550-557 (2004).
-
(2004)
J. Med. Chem.
, vol.47
, Issue.3
, pp. 550-557
-
-
Weber, A.1
Casini, A.2
Heine, A.3
-
67
-
-
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 5(8), e12214 (2010).
-
(2010)
Plos ONE
, vol.5
, Issue.8
-
-
De Franchi, E.1
Schalon, C.2
Messa, M.3
Onofri, F.4
Benfenati, F.5
Rognan, D.6
-
68
-
-
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. 46(2), 717-727 (2006).
-
(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
-
69
-
-
44349119204
-
A simple and fuzzy method to align and compare druggable ligand-binding sites
-
Schalon C, Surgand JS, Kellenberger E, Rognan D. A simple and fuzzy method to align and compare druggable ligand-binding sites. Prot. Struct. Funct. Bioinform. 71(4), 1755-1778 (2008).
-
(2008)
Prot. Struct. Funct. Bioinform.
, vol.71
, Issue.4
, pp. 1755-1778
-
-
Schalon, C.1
Surgand, J.S.2
Kellenberger, E.3
Rognan, D.4
-
70
-
-
68249144628
-
Drug discovery using chemical systems biology: Repositioning the safe medicine comtan to treat multi-drug and extensively drug resistant tuberculosis
-
Kinnings SL, Liu N, Buchmeier N, Tonge PJ, Xie L, Bourne PE. Drug discovery using chemical systems biology: repositioning the safe medicine comtan to treat multi-drug and extensively drug resistant tuberculosis. PloS Comput. Biol. 5(7), e1000423 (2009).
-
(2009)
PloS Comput. Biol.
, vol.5
, Issue.7
-
-
Kinnings, S.L.1
Liu, N.2
Buchmeier, N.3
Tonge, P.J.4
Xie, L.5
Bourne, P.E.6
-
71
-
-
0042890523
-
Inferring functional relationships of proteins from local sequence and spatial surface patterns
-
Binkowski TA, Adamian L, Liang J. Inferring functional relationships of proteins from local sequence and spatial surface patterns. J. Mol. Biol. 332(2), 505-526 (2003).
-
(2003)
J. Mol. Biol.
, vol.332
, Issue.2
, pp. 505-526
-
-
Binkowski, T.A.1
Adamian, L.2
Liang, J.3
-
72
-
-
44949110143
-
Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions
-
Minai R, Matsuo Y, Onuki H, Hirota H. Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions. Prot. Struct. Func. Bioinform. 72(1), 367-381 (2008).
-
(2008)
Prot. Struct. Func. Bioinform.
, vol.72
, Issue.1
, pp. 367-381
-
-
Minai, R.1
Matsuo, Y.2
Onuki, H.3
Hirota, H.4
-
73
-
-
33845306506
-
Protein structure similarity clustering: Dynamic treatment of PDB structures facilitates clustering
-
Charette BD, MacDonald RG, Wetzel S, Berkowitz DB, Waldmann H. Protein structure similarity clustering: dynamic treatment of PDB structures facilitates clustering. Angew. Chem. Int. Ed. 45(46), 7766-7770 (2006).
-
(2006)
Angew. Chem. Int. Ed.
, vol.45
, Issue.46
, pp. 7766-7770
-
-
Charette, B.D.1
MacDonald, R.G.2
Wetzel, S.3
Berkowitz, D.B.4
Waldmann, H.5
-
74
-
-
17044421362
-
Protein structure similarity clustering and natural product structure as guiding principles in drug discovery
-
Koch MA, Waldmann H. Protein structure similarity clustering and natural product structure as guiding principles in drug discovery. Drug Discov. Today 10(7), 471-483 (2005).
-
(2005)
Drug Discov. Today
, vol.10
, Issue.7
, pp. 471-483
-
-
Koch, M.A.1
Waldmann, H.2
-
75
-
-
10044253102
-
Compound library development guided by protein structure similarity clustering and natural product structure
-
Koch MA, Wittenberg LO, Basu S et al. Compound library development guided by protein structure similarity clustering and natural product structure. Proc. Natl Acad. Sci. USA 101(48), 16721-16726 (2004).
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, Issue.48
, pp. 16721-16726
-
-
Koch, M.A.1
Wittenberg, L.O.2
Basu, S.3
-
76
-
-
58949090837
-
ATP competitive inhibitors of d-alanine-d-alanine ligase based on protein kinase inhibitor scaffolds
-
Triola G, Wetzel S, Ellinger B et al. ATP competitive inhibitors of d-alanine-d-alanine ligase based on protein kinase inhibitor scaffolds. Bioorg. Med. Chem. 17(3), 1079-1087 (2009).
-
(2009)
Bioorg. Med. Chem.
, vol.17
, Issue.3
, pp. 1079-1087
-
-
Triola, G.1
Wetzel, S.2
Ellinger, B.3
-
77
-
-
84891747045
-
-
SiteEngine. http://bioinfo3d.cs.tau.ac.il/SiteEngine
-
-
-
-
78
-
-
84891736818
-
-
PoSSum. http://possum.cbrc.jp/PoSSuM
-
-
-
-
79
-
-
84891739022
-
-
SourceForge. Druggable Cavity Directory. http://fpocket.sourceforge.net/ dcd
-
-
-
|