-
1
-
-
84859179256
-
Exploring Activity Cliffs in Medicinal Chemistry
-
Stumpfe, D.; Bajorath, J. Exploring Activity Cliffs in Medicinal Chemistry J. Med. Chem. 2012, 55, 2932-2942
-
(2012)
J. Med. Chem.
, vol.55
, pp. 2932-2942
-
-
Stumpfe, D.1
Bajorath, J.2
-
2
-
-
84892612846
-
Recent Progress in Understanding Activity Cliffs and Their Utility in Medicinal Chemistry
-
Stumpfe, D.; Hu, Y.; Dimova, D.; Bajorath, J. Recent Progress in Understanding Activity Cliffs and Their Utility in Medicinal Chemistry J. Med. Chem. 2014, 57, 18-28
-
(2014)
J. Med. Chem.
, vol.57
, pp. 18-28
-
-
Stumpfe, D.1
Hu, Y.2
Dimova, D.3
Bajorath, J.4
-
3
-
-
70350507116
-
Structural Interpretation of Activity Cliffs Revealed by Systematic Analysis of Structure-Activity Relationships in Analog Series
-
Sisay, M. T.; Peltason, L.; Bajorath, J. Structural Interpretation of Activity Cliffs Revealed by Systematic Analysis of Structure-Activity Relationships in Analog Series J. Chem. Inf. Model. 2009, 49, 2179-2189
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 2179-2189
-
-
Sisay, M.T.1
Peltason, L.2
Bajorath, J.3
-
4
-
-
80052080825
-
From Activity Cliffs to Target-Specific Scoring Models and Pharmacophore Hypotheses
-
Seebeck, B.; Wagener, M.; Rarey, M. From Activity Cliffs to Target-Specific Scoring Models and Pharmacophore Hypotheses ChemMedChem 2011, 6, 1630-1639
-
(2011)
ChemMedChem
, vol.6
, pp. 1630-1639
-
-
Seebeck, B.1
Wagener, M.2
Rarey, M.3
-
5
-
-
42149090634
-
Structure-Activity Landscape Index: Identifying and Quantifying Activity Cliffs
-
Guha, R.; Van Drie, J. H. Structure-Activity Landscape Index: Identifying and Quantifying Activity Cliffs J. Chem. Inf. Model. 2008, 48, 646-658
-
(2008)
J. Chem. Inf. Model.
, vol.48
, pp. 646-658
-
-
Guha, R.1
Van Drie, J.H.2
-
6
-
-
84859169320
-
Exploration of 3D Activity Cliffs on the Basis of Compound Binding Modes and Comparison of 2D and 3D cliffs
-
Hu, Y.; Bajorath, J. Exploration of 3D Activity Cliffs on the Basis of Compound Binding Modes and Comparison of 2D and 3D cliffs J. Chem. Inf. Model. 2012, 52, 670-677
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 670-677
-
-
Hu, Y.1
Bajorath, J.2
-
7
-
-
34248576316
-
Molecular Similarity Analysis Uncovers the Presence of Heterogeneous Structure-Activity Relationships and Variable Activity Landscapes within Active Sites
-
Peltason, L.; Bajorath, J. Molecular Similarity Analysis Uncovers the Presence of Heterogeneous Structure-Activity Relationships and Variable Activity Landscapes within Active Sites Chem. Biol. 2007, 14, 489-497
-
(2007)
Chem. Biol.
, vol.14
, pp. 489-497
-
-
Peltason, L.1
Bajorath, J.2
-
8
-
-
84855757480
-
-
Chemical Computing Group Inc. Montreal, Quebec, Canada.
-
Molecular Operating Environment; Chemical Computing Group Inc.: Montreal, Quebec, Canada, 2010.
-
(2010)
Molecular Operating Environment
-
-
-
9
-
-
84862854379
-
Systematic Identification and Classification of Three-Dimensional Activity Cliffs
-
Hu, Y.; Furtmann, N.; Gütschow, M.; Bajorath, J. Systematic Identification and Classification of Three-Dimensional Activity Cliffs J. Chem. Inf. Model. 2012, 52, 1490-1498
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 1490-1498
-
-
Hu, Y.1
Furtmann, N.2
Gütschow, M.3
Bajorath, J.4
-
10
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28, 235-242
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
11
-
-
84893065058
-
KLIFS: A Knowledge-Based Structural Database to Navigate Kinase-Ligand Interaction Space
-
van Linden, O. P.; Kooistra, A. J.; Leurs, R.; de Esch, I. J.; de Graaf, C. KLIFS: A Knowledge-Based Structural Database to Navigate Kinase-Ligand Interaction Space J. Med. Chem. 2014, 57, 249-277
-
(2014)
J. Med. Chem.
, vol.57
, pp. 249-277
-
-
Van Linden, O.P.1
Kooistra, A.J.2
Leurs, R.3
De Esch, I.J.4
De Graaf, C.5
-
12
-
-
84871730931
-
Approaches to Discover Non-ATP Site Kinase Inhibitors
-
Gavrin, L. K.; Saiah, E. Approaches to Discover Non-ATP Site Kinase Inhibitors Med. Chem. Commun. 2013, 4, 41-51
-
(2013)
Med. Chem. Commun.
, vol.4
, pp. 41-51
-
-
Gavrin, L.K.1
Saiah, E.2
-
13
-
-
84903208494
-
Exploration of Type II Binding Mode: A Privileged Approach for Kinase Inhibitor Focused Drug Discovery?
-
Zhao, Z.; Wu, H.; Wang, L.; Liu, Y.; Knapp, S.; Liu, Q.; Gray, N. S. Exploration of Type II Binding Mode: A Privileged Approach for Kinase Inhibitor Focused Drug Discovery? ACS Chem. Biol. 2014, 9, 1230-1241
-
(2014)
ACS Chem. Biol.
, vol.9
, pp. 1230-1241
-
-
Zhao, Z.1
Wu, H.2
Wang, L.3
Liu, Y.4
Knapp, S.5
Liu, Q.6
Gray, N.S.7
-
14
-
-
19744365702
-
A Small Molecule-Kinase Interaction Map for Clinical Kinase Inhibitors
-
Fabian, M. A.; Biggs, W. H., III; Treiber, D. K.; Atteridge, C. E.; Azimioara, M. D.; Benedetti, M. G.; Carter, T. A.; Ciceri, P.; Edeen, P. T.; Floyd, M.; Ford, J. M.; Galvin, M.; Gerlach, J. L.; Grotzfeld, R. M.; Herrgard, S.; Insko, D. E.; Insko, M. A.; Lai, A. G.; Lélias, J. M.; Mehta, S. A.; Milanov, Z. V.; Velasco, A. M.; Wodicka, L. M.; Patel, H. K.; Zarrinkar, P. P.; Lockhart, D. J. A Small Molecule-Kinase Interaction Map for Clinical Kinase Inhibitors Nature Biotechnol. 2005, 23, 329-336
-
(2005)
Nature Biotechnol.
, vol.23
, pp. 329-336
-
-
Fabian, M.A.1
Biggs, W.H.2
Treiber, D.K.3
Atteridge, C.E.4
Azimioara, M.D.5
Benedetti, M.G.6
Carter, T.A.7
Ciceri, P.8
Edeen, P.T.9
Floyd, M.10
Ford, J.M.11
Galvin, M.12
Gerlach, J.L.13
Grotzfeld, R.M.14
Herrgard, S.15
Insko, D.E.16
Insko, M.A.17
Lai, A.G.18
Lélias, J.M.19
Mehta, S.A.20
Milanov, Z.V.21
Velasco, A.M.22
Wodicka, L.M.23
Patel, H.K.24
Zarrinkar, P.P.25
Lockhart, D.J.26
more..
-
15
-
-
38049018155
-
A Quantitative Analysis of Kinase Inhibitor Selectivity
-
Karaman, M. W.; Herrgard, S.; Treiber, D. K.; Gallant, P.; Atteridge, C. E.; Campbell, B. T.; Chan, K. W.; Ciceri, P.; Davis, M. I.; Edeen, P. T.; Faraoni, R.; Floyd, M.; Hunt, J. P.; Lockhart, D. J.; Milanov, Z. V.; Morrison, M. J.; Pallares, G.; Patel, H. K.; Pritchard, S.; Wodicka, L. M.; Zarrinkar, P. P. A Quantitative Analysis of Kinase Inhibitor Selectivity Nature Biotechnol. 2008, 26, 127-132
-
(2008)
Nature Biotechnol.
, vol.26
, pp. 127-132
-
-
Karaman, M.W.1
Herrgard, S.2
Treiber, D.K.3
Gallant, P.4
Atteridge, C.E.5
Campbell, B.T.6
Chan, K.W.7
Ciceri, P.8
Davis, M.I.9
Edeen, P.T.10
Faraoni, R.11
Floyd, M.12
Hunt, J.P.13
Lockhart, D.J.14
Milanov, Z.V.15
Morrison, M.J.16
Pallares, G.17
Patel, H.K.18
Pritchard, S.19
Wodicka, L.M.20
Zarrinkar, P.P.21
more..
-
16
-
-
78649340278
-
Activation State-Dependent Binding of Small Molecule Kinase Inhibitors: Structural Insights from Biochemistry
-
Wodicka, L. M.; Ciceri, P.; Davis, M. I.; Hunt, J. P.; Floyd, M.; Salerno, S.; Hua, X. H.; Ford, J. M.; Armstrong, R. C.; Zarrinkar, P. P.; Treiber, D. K. Activation State-Dependent Binding of Small Molecule Kinase Inhibitors: Structural Insights from Biochemistry Chem. Biol. 2010, 17, 1241-1249
-
(2010)
Chem. Biol.
, vol.17
, pp. 1241-1249
-
-
Wodicka, L.M.1
Ciceri, P.2
Davis, M.I.3
Hunt, J.P.4
Floyd, M.5
Salerno, S.6
Hua, X.H.7
Ford, J.M.8
Armstrong, R.C.9
Zarrinkar, P.P.10
Treiber, D.K.11
-
17
-
-
84860833500
-
Reorganizing the Protein Space at the Universal Protein Resource (UniProt)
-
UniProt Consortium
-
UniProt Consortium Reorganizing the Protein Space at the Universal Protein Resource (UniProt) Nucleic Acids Res. 2012, 40, D142-D148
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 142-D148
-
-
-
18
-
-
0242490780
-
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
-
Shannon, P.; Markiel, A.; Ozier, O.; Baliga, N. S.; Wang, J. T.; Ramage, D.; Amin, N.; Schwikowski, B.; Ideker, T. Cytoscape: a Software Environment for Integrated Models of Biomolecular Interaction Networks Genome Res. 2003, 13, 2498-2504
-
(2003)
Genome Res.
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
19
-
-
85016377807
-
Structure Modification in Chemical Databases
-
In; Oprea, T. I. Wiley-VCH: Weinheim, Germany
-
Kenny, P. W.; Sadowski, J. Structure Modification in Chemical Databases. In Chemoinformatics in Drug Discovery; Oprea, T. I., Ed.; Wiley-VCH: Weinheim, Germany, 2004; pp 271-285.
-
(2004)
Chemoinformatics in Drug Discovery
, pp. 271-285
-
-
Kenny, P.W.1
Sadowski, J.2
-
20
-
-
77949848865
-
Computationally Efficient Algorithm to Identify Matched Molecular Pairs (MMPs) in Large Data Sets
-
Hussain, J.; Rea, C. Computationally Efficient Algorithm to Identify Matched Molecular Pairs (MMPs) in Large Data Sets J. Chem. Inf. Model. 2010, 50, 339-348
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 339-348
-
-
Hussain, J.1
Rea, C.2
-
21
-
-
84861503290
-
MMP-Cliffs: Systematic Identification of Activity Cliffs on the Basis of Matched Molecular Pairs
-
Hu, X.; Hu, Y.; Vogt, M.; Stumpfe, D.; Bajorath, J. MMP-Cliffs: Systematic Identification of Activity Cliffs on the Basis of Matched Molecular Pairs J. Chem. Inf. Model. 2012, 52, 1138-1145
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 1138-1145
-
-
Hu, X.1
Hu, Y.2
Vogt, M.3
Stumpfe, D.4
Bajorath, J.5
-
22
-
-
85067743313
-
-
version 1.7.7; OpenEye Scientific Software, Inc. Santa Fe, NM.
-
OEChem, version 1.7.7; OpenEye Scientific Software, Inc.: Santa Fe, NM, 2012; http://www.eyesopen.com.
-
(2012)
OEChem
-
-
-
23
-
-
84862192766
-
ChEMBL: A Large-Scale Bioactivity Database for Drug Discovery
-
Gaulton, A.; Bellis, L. J.; Bento, A. P.; Chambers, J.; Davies, M.; Hersey, A.; Light, Y.; McGlinchey, S.; Michalovich, D.; Al-Lazikani, B.; Overington, J. P. ChEMBL: A Large-Scale Bioactivity Database for Drug Discovery Nucleic Acids Res. 2011, 40, D1100-D1107
-
(2011)
Nucleic Acids Res.
, vol.40
, pp. 1100-D1107
-
-
Gaulton, A.1
Bellis, L.J.2
Bento, A.P.3
Chambers, J.4
Davies, M.5
Hersey, A.6
Light, Y.7
McGlinchey, S.8
Michalovich, D.9
Al-Lazikani, B.10
Overington, J.P.11
-
24
-
-
85067762523
-
-
DOI.
-
Furtmann, N.; Hu, Y.; Bajorath, J. Classification of Binding Modes for Kinase-Inhibitor Complex Structures, 3D Activity Cliffs Formed by Kinase Inhibitors, and Structural Analogues of 3D-Cliff Compounds. ZENODO. DOI: 10.5281/zenodo.11022.
-
Classification of Binding Modes for Kinase-Inhibitor Complex Structures, 3D Activity Cliffs Formed by Kinase Inhibitors, and Structural Analogues of 3D-Cliff Compounds. ZENODO
-
-
Furtmann, N.1
Hu, Y.2
Bajorath, J.3
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