-
1
-
-
84978768131
-
Evidence-based and quantitative prioritization of tool compounds in phenotypic drug discovery
-
Wang, Y., et al. Evidence-based and quantitative prioritization of tool compounds in phenotypic drug discovery. Cell Chem. Biol. 23 (2016), 862–874.
-
(2016)
Cell Chem. Biol.
, vol.23
, pp. 862-874
-
-
Wang, Y.1
-
2
-
-
84876933802
-
Shifting from the single to the multitarget paradigm in drug discovery
-
Medina-Franco, J.L., et al. Shifting from the single to the multitarget paradigm in drug discovery. Drug Discov. Today 18 (2013), 495–501.
-
(2013)
Drug Discov. Today
, vol.18
, pp. 495-501
-
-
Medina-Franco, J.L.1
-
3
-
-
84899149579
-
Drug2Gene: an exhaustive resource to explore effectively the drug–target relation network
-
Roider, H.G., et al. Drug2Gene: an exhaustive resource to explore effectively the drug–target relation network. BMC Bioinf., 15, 2014, 68.
-
(2014)
BMC Bioinf.
, vol.15
, pp. 68
-
-
Roider, H.G.1
-
4
-
-
84976897983
-
STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data
-
Szklarczyk, D., et al. STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Res. 44 (2016), D380–D384.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D380-D384
-
-
Szklarczyk, D.1
-
5
-
-
0031710509
-
Chemical genetics resulting from a passion for synthetic organic chemistry
-
Schreiber, S.L., Chemical genetics resulting from a passion for synthetic organic chemistry. Bioorg. Med. Chem. 6 (1998), 1127–1152.
-
(1998)
Bioorg. Med. Chem.
, vol.6
, pp. 1127-1152
-
-
Schreiber, S.L.1
-
6
-
-
11144298973
-
Exploring biology with small organic molecules
-
Stockwell, B.R., Exploring biology with small organic molecules. Nature 432 (2004), 846–854.
-
(2004)
Nature
, vol.432
, pp. 846-854
-
-
Stockwell, B.R.1
-
8
-
-
84870774465
-
Reducing safety-related drug attrition: the use of in vitro pharmacological profiling
-
Bowes, J., et al. Reducing safety-related drug attrition: the use of in vitro pharmacological profiling. Nat. Rev. Drug Discov. 11 (2012), 909–922.
-
(2012)
Nat. Rev. Drug Discov.
, vol.11
, pp. 909-922
-
-
Bowes, J.1
-
9
-
-
84878771632
-
WOMBAT and WOMBAT-PK: bioactivity databases for lead and drug discovery
-
S.L. Schreiber Wiley-VCH
-
Olah, M., et al. WOMBAT and WOMBAT-PK: bioactivity databases for lead and drug discovery. Schreiber, S.L., (eds.) Chemical Biology: From Small Molecules to Systems Biology and Drug Design, 2007, Wiley-VCH, 760–786.
-
(2007)
Chemical Biology: From Small Molecules to Systems Biology and Drug Design
, pp. 760-786
-
-
Olah, M.1
-
10
-
-
84891762026
-
The ChEMBL bioactivity database: an update
-
Bento, A.P., et al. The ChEMBL bioactivity database: an update. Nucleic Acids Res. 42 (2014), D1083–D1090.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D1083-D1090
-
-
Bento, A.P.1
-
11
-
-
2542530042
-
The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures
-
Wang, R., et al. The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J. Med. Chem. 47 (2004), 2977–2980.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 2977-2980
-
-
Wang, R.1
-
12
-
-
84891791940
-
The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands
-
Pawson, A.J., et al. The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands. Nucleic Acids Res. 42 (2014), D1098–D1106.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D1098-D1106
-
-
Pawson, A.J.1
-
13
-
-
84946035207
-
BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types
-
Howe, E.A., et al. BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types. Nucleic Acids Res. 43 (2015), D1163–D1170.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D1163-D1170
-
-
Howe, E.A.1
-
14
-
-
84939257632
-
Cross-mapping of protein – ligand binding data between ChEMBL and PDBbind
-
Liu, Z.H., et al. Cross-mapping of protein – ligand binding data between ChEMBL and PDBbind. Mol. Inf. 34 (2015), 568–576.
-
(2015)
Mol. Inf.
, vol.34
, pp. 568-576
-
-
Liu, Z.H.1
-
15
-
-
84884590180
-
Big pharma screening collections: more of the same or unique libraries? The AstraZeneca-Bayer Pharma AG case
-
Kogej, T., et al. Big pharma screening collections: more of the same or unique libraries? The AstraZeneca-Bayer Pharma AG case. Drug Discov. Today 18 (2013), 1014–1024.
-
(2013)
Drug Discov. Today
, vol.18
, pp. 1014-1024
-
-
Kogej, T.1
-
16
-
-
84876725194
-
InChI — the worldwide chemical structure identifier standard
-
Heller, S., et al. InChI — the worldwide chemical structure identifier standard. J. Cheminf., 5, 2013, 7.
-
(2013)
J. Cheminf.
, vol.5
, pp. 7
-
-
Heller, S.1
-
17
-
-
0037252705
-
Database resources of the National Center for Biotechnology
-
Wheeler, D.L., et al. Database resources of the National Center for Biotechnology. Nucleic Acids Res. 31 (2003), 28–33.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 28-33
-
-
Wheeler, D.L.1
-
18
-
-
85016153986
-
UniProt: the universal protein knowledgebase
-
UniProt Consortium, UniProt: the universal protein knowledgebase. Nucleic Acids Res. 45 (2017), D158–D169.
-
(2017)
Nucleic Acids Res.
, vol.45
, pp. D158-D169
-
-
UniProt Consortium1
-
19
-
-
0037249501
-
PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification
-
Thomas, P.D., et al. PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res. 31 (2003), 334–341.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 334-341
-
-
Thomas, P.D.1
-
20
-
-
84891760956
-
Data, information, knowledge and principle: back to metabolism in KEGG
-
Kanehisa, M., et al. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42 (2014), D199–D205.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D199-D205
-
-
Kanehisa, M.1
-
21
-
-
0034069495
-
Gene ontology: tool for the unification of biology: The Gene Ontology Consortium
-
Ashburner, M., et al. Gene ontology: tool for the unification of biology: The Gene Ontology Consortium. Nat. Genet. 25 (2000), 25–29.
-
(2000)
Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
-
22
-
-
70349570566
-
Manual annotation of protein interactions
-
Bureeva, S., et al. Manual annotation of protein interactions. Methods Mol. Biol. 563 (2009), 75–95.
-
(2009)
Methods Mol. Biol.
, vol.563
, pp. 75-95
-
-
Bureeva, S.1
-
23
-
-
0037598287
-
Finding the molecules to fuel chemogenomics
-
Namchuk, M.N., Finding the molecules to fuel chemogenomics. Targets 1 (2002), 125–129.
-
(2002)
Targets
, vol.1
, pp. 125-129
-
-
Namchuk, M.N.1
-
24
-
-
84885904434
-
The CARLSBAD database: a confederated database of chemical bioactivities
-
bat044
-
Mathias, S.L., et al. The CARLSBAD database: a confederated database of chemical bioactivities. Database, 2013, 2013 bat044.
-
(2013)
Database
, vol.2013
-
-
Mathias, S.L.1
-
25
-
-
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. 39 (1996), 2887–2893.
-
(1996)
J. Med. Chem.
, vol.39
, pp. 2887-2893
-
-
Bemis, G.W.1
Murcko, M.A.2
-
26
-
-
77952772341
-
Extended-connectivity fingerprints
-
Rogers, D., Hahn, M., Extended-connectivity fingerprints. J. Chem. Inf. Model. 50 (2010), 742–754.
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 742-754
-
-
Rogers, D.1
Hahn, M.2
-
27
-
-
0023965741
-
Smiles, a Chemical Language and Information-System. 1. Introduction to methodology and encoding rules
-
Weininger, D., Smiles, a Chemical Language and Information-System. 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 28 (1988), 31–36.
-
(1988)
J. Chem. Inf. Comput. Sci.
, vol.28
, pp. 31-36
-
-
Weininger, D.1
-
28
-
-
33745391215
-
Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases
-
Nidhi, et al. Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases. J. Chem. Inf. Model. 46 (2006), 1124–1133.
-
(2006)
J. Chem. Inf. Model.
, vol.46
, pp. 1124-1133
-
-
Nidhi1
-
29
-
-
85016031495
-
Chemometric applications of naïve Bayesian models in drug discovery
-
J. Bajorath John Wiley & Sons
-
Lounkine, E., et al. Chemometric applications of naïve Bayesian models in drug discovery. Bajorath, J., (eds.) Chemoinformatics for Drug Discovery, 2013, John Wiley & Sons, 131–148.
-
(2013)
Chemoinformatics for Drug Discovery
, pp. 131-148
-
-
Lounkine, E.1
-
30
-
-
84996605707
-
The evolution of drug design at Merck Research Laboratories
-
Brown, F.K., et al. The evolution of drug design at Merck Research Laboratories. J. Comput. Aided Mol. Des. 31 (2017), 255–266.
-
(2017)
J. Comput. Aided Mol. Des.
, vol.31
, pp. 255-266
-
-
Brown, F.K.1
-
31
-
-
33750986884
-
‘Bayes affinity fingerprints’ improve retrieval rates in virtual screening and define orthogonal bioactivity space: When are multitarget drugs a feasible concept?
-
Bender, A., et al. ‘Bayes affinity fingerprints’ improve retrieval rates in virtual screening and define orthogonal bioactivity space: When are multitarget drugs a feasible concept?. J. Chem. Inf. Model. 46 (2006), 2445–2456.
-
(2006)
J. Chem. Inf. Model.
, vol.46
, pp. 2445-2456
-
-
Bender, A.1
-
32
-
-
10044263240
-
Similarity to molecules in the training set is a good discriminator for prediction accuracy in QSAR
-
Sheridan, R.P., et al. Similarity to molecules in the training set is a good discriminator for prediction accuracy in QSAR. J. Chem. Inf. Comput. Sci. 44 (2004), 1912–1928.
-
(2004)
J. Chem. Inf. Comput. Sci.
, vol.44
, pp. 1912-1928
-
-
Sheridan, R.P.1
-
33
-
-
84862237958
-
MetaBase—the wiki-database of biological databases
-
Bolser, D.M., et al. MetaBase—the wiki-database of biological databases. Nucleic Acids Res. 40 (2012), D1250–D1254.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D1250-D1254
-
-
Bolser, D.M.1
-
34
-
-
84923367417
-
Deep neural nets as a method for quantitative structure-activity relationships
-
Ma, J., et al. Deep neural nets as a method for quantitative structure-activity relationships. J. Chem. Inf. Model. 55 (2015), 263–274.
-
(2015)
J. Chem. Inf. Model.
, vol.55
, pp. 263-274
-
-
Ma, J.1
-
35
-
-
84927735077
-
Massively Multitask Networks for Drug Discovery
-
Cornell University Library
-
Ramsundar, B., et al. Massively Multitask Networks for Drug Discovery. 2015, Cornell University Library.
-
(2015)
-
-
Ramsundar, B.1
-
36
-
-
84894641359
-
Enrichment analysis for discovering biological associations in phenotypic screens
-
Polyakov, V.R., et al. Enrichment analysis for discovering biological associations in phenotypic screens. J. Chem. Inf. Model. 54 (2014), 377–386.
-
(2014)
J. Chem. Inf. Model.
, vol.54
, pp. 377-386
-
-
Polyakov, V.R.1
-
37
-
-
84996843153
-
Understanding cytotoxicity and cytostaticity in a high-throughput screening collection
-
Mervin, L.H., et al. Understanding cytotoxicity and cytostaticity in a high-throughput screening collection. ACS Chem. Biol. 11 (2016), 3007–3023.
-
(2016)
ACS Chem. Biol.
, vol.11
, pp. 3007-3023
-
-
Mervin, L.H.1
-
38
-
-
84939958419
-
The opportunities of mining historical and collective data in drug discovery
-
Wassermann, A.M., et al. The opportunities of mining historical and collective data in drug discovery. Drug Discov. Today 20 (2015), 422–434.
-
(2015)
Drug Discov. Today
, vol.20
, pp. 422-434
-
-
Wassermann, A.M.1
-
39
-
-
84902201072
-
The role of historical bioactivity data in the deconvolution of phenotypic screens
-
Bornot, A., et al. The role of historical bioactivity data in the deconvolution of phenotypic screens. J. Biomol. Screen. 19 (2014), 696–706.
-
(2014)
J. Biomol. Screen.
, vol.19
, pp. 696-706
-
-
Bornot, A.1
-
40
-
-
84881116194
-
Systematic identification of proteins that elicit drug side effects
-
Kuhn, M., et al. Systematic identification of proteins that elicit drug side effects. Mol Syst Biol., 9, 2013, 663.
-
(2013)
Mol Syst Biol.
, vol.9
, pp. 663
-
-
Kuhn, M.1
-
41
-
-
84904731398
-
Composition and applications of focus libraries to phenotypic assays
-
Wassermann, A.M., et al. Composition and applications of focus libraries to phenotypic assays. Front. Pharmacol., 5, 2014, 164.
-
(2014)
Front. Pharmacol.
, vol.5
, pp. 164
-
-
Wassermann, A.M.1
-
42
-
-
77249142404
-
The art of the chemical probe
-
Frye, S.V., The art of the chemical probe. Nat. Chem. Biol. 6 (2010), 159–161.
-
(2010)
Nat. Chem. Biol.
, vol.6
, pp. 159-161
-
-
Frye, S.V.1
-
43
-
-
84875457503
-
The why and how of phenotypic small-molecule screens
-
Eggert, U.S., The why and how of phenotypic small-molecule screens. Nat. Chem. Biol. 9 (2013), 206–209.
-
(2013)
Nat. Chem. Biol.
, vol.9
, pp. 206-209
-
-
Eggert, U.S.1
-
44
-
-
84863317657
-
Novel aspects of mevalonate pathway inhibitors as antitumor agents
-
Thurnher, M., et al. Novel aspects of mevalonate pathway inhibitors as antitumor agents. Clin. Cancer Res. 18 (2012), 3524–3531.
-
(2012)
Clin. Cancer Res.
, vol.18
, pp. 3524-3531
-
-
Thurnher, M.1
-
45
-
-
77953193637
-
Analysis of kinase inhibitor selectivity using a thermodynamics-based partition index
-
Cheng, A.C., et al. Analysis of kinase inhibitor selectivity using a thermodynamics-based partition index. J. Med. Chem. 53 (2010), 4502–4510.
-
(2010)
J. Med. Chem.
, vol.53
, pp. 4502-4510
-
-
Cheng, A.C.1
-
46
-
-
36148943501
-
Gini coefficient: a new way to express selectivity of kinase inhibitors against a family of kinases
-
Graczyk, P.P., Gini coefficient: a new way to express selectivity of kinase inhibitors against a family of kinases. J. Med. Chem. 50 (2007), 5773–5779.
-
(2007)
J. Med. Chem.
, vol.50
, pp. 5773-5779
-
-
Graczyk, P.P.1
-
47
-
-
79953837902
-
A theoretical entropy score as a single value to express inhibitor selectivity
-
Uitdehaag, J.C., Zaman, G.J., A theoretical entropy score as a single value to express inhibitor selectivity. BMC Bioinf., 12, 2011, 94.
-
(2011)
BMC Bioinf.
, vol.12
, pp. 94
-
-
Uitdehaag, J.C.1
Zaman, G.J.2
-
48
-
-
68949147006
-
Measuring and interpreting the selectivity of protein kinase inhibitors
-
Smyth, L.A., Collins, I., Measuring and interpreting the selectivity of protein kinase inhibitors. J. Chem. Biol. 2 (2009), 131–151.
-
(2009)
J. Chem. Biol.
, vol.2
, pp. 131-151
-
-
Smyth, L.A.1
Collins, I.2
-
49
-
-
84866261609
-
Chemotography for multi-target SAR analysis in the context of biological pathways
-
Lounkine, E., et al. Chemotography for multi-target SAR analysis in the context of biological pathways. Bioorg. Med. Chem. 20 (2012), 5416–5427.
-
(2012)
Bioorg. Med. Chem.
, vol.20
, pp. 5416-5427
-
-
Lounkine, E.1
-
50
-
-
13444292249
-
Using genome-wide transcriptional profiling to elucidate small-molecule mechanism
-
Butcher, R.A., Schreiber, S.L., Using genome-wide transcriptional profiling to elucidate small-molecule mechanism. Curr. Opin. Chem. Biol. 9 (2005), 25–30.
-
(2005)
Curr. Opin. Chem. Biol.
, vol.9
, pp. 25-30
-
-
Butcher, R.A.1
Schreiber, S.L.2
-
51
-
-
85015335626
-
Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes
-
1757–1174
-
Bray, M.A., et al. Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. Nat. Protoc., 11, 2016 1757–1174.
-
(2016)
Nat. Protoc.
, vol.11
-
-
Bray, M.A.1
-
52
-
-
84891388151
-
Multiplex cytological profiling assay to measure diverse cellular states
-
Gustafsdottir, S.M., et al. Multiplex cytological profiling assay to measure diverse cellular states. PLoS One, 8, 2013, e80999.
-
(2013)
PLoS One
, vol.8
, pp. e80999
-
-
Gustafsdottir, S.M.1
-
53
-
-
63849172494
-
Identifying the proteins to which small-molecule probes and drugs bind in cells
-
Ong, S.E., et al. Identifying the proteins to which small-molecule probes and drugs bind in cells. Proc. Natl. Acad. Sci. U. S. A. 106 (2009), 4617–4622.
-
(2009)
Proc. Natl. Acad. Sci. U. S. A.
, vol.106
, pp. 4617-4622
-
-
Ong, S.E.1
-
54
-
-
84906702408
-
RNAi screening comes of age: improved techniques and complementary approaches
-
Mohr, S.E., et al. RNAi screening comes of age: improved techniques and complementary approaches. Nat. Rev. Mol. Cell Biol. 15 (2014), 591–600.
-
(2014)
Nat. Rev. Mol. Cell Biol.
, vol.15
, pp. 591-600
-
-
Mohr, S.E.1
-
55
-
-
84913594397
-
Genome editing. The new frontier of genome engineering with CRISPR-Cas9
-
Doudna, J.A., Charpentier, E., Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science, 346, 2014, 1258096.
-
(2014)
Science
, vol.346
, pp. 1258096
-
-
Doudna, J.A.1
Charpentier, E.2
|