-
1
-
-
84903752225
-
Data-driven medicinal chemistry in the era of big data
-
Lusher, S. J., McGuire, R., van Schaik, R. C., Nicholson, C. D., and de Vlieg, J. (2014) Data-driven medicinal chemistry in the era of big data. Drug Discovery Today 19(7), 859-868.
-
(2014)
Drug Discovery Today
, vol.19
, Issue.7
, pp. 859-868
-
-
Lusher, S.J.1
McGuire, R.2
Van Schaik, R.C.3
Nicholson, C.D.4
De Vlieg, J.5
-
2
-
-
84931270668
-
Concepts and applications of molecular similarity
-
Johnson, M. A., and Maggiora, G. (1992) Concepts and applications of molecular similarity. J. Comput. Chem. 13(4), 539-540.
-
(1992)
J. Comput. Chem.
, vol.13
, Issue.4
, pp. 539-540
-
-
Johnson, M.A.1
Maggiora, G.2
-
3
-
-
0038170311
-
Similarity metrics for ligands reflecting the similarity of the target proteins
-
Schuffenhauer, A., Floersheim, P., Acklin, P., and Jacoby, E. (2003) Similarity metrics for ligands reflecting the similarity of the target proteins. J. Chem. Inf. Comput. Sci. 43(2), 391-405.
-
(2003)
J. Chem. Inf. Comput. Sci.
, vol.43
, Issue.2
, pp. 391-405
-
-
Schuffenhauer, A.1
Floersheim, P.2
Acklin, P.3
Jacoby, E.4
-
4
-
-
33750994920
-
Bridging chemical and biological space: "target fishing" using 2D and 3D molecular descriptors
-
Nettles, J. H., Jenkins, J. L., Bender, A., Deng, Z., Davies, J. W., and Glick, M. (2006) Bridging chemical and biological space: "target fishing" using 2D and 3D molecular descriptors. J. Med. Chem. 49(23), 6802-6810.
-
(2006)
J. Med. Chem.
, vol.49
, Issue.23
, pp. 6802-6810
-
-
Nettles, J.H.1
Jenkins, J.L.2
Bender, A.3
Deng, Z.4
Davies, J.W.5
Glick, M.6
-
5
-
-
33846518797
-
In silico target fishing: Predicting biological targets from chemical structure
-
Jenkins, J. L., Bender, A., and Davies, J. W. (2006) In silico target fishing: Predicting biological targets from chemical structure. Drug Discovery Today: Technol. 3(4), 413-421.
-
(2006)
Drug Discovery Today: Technol
, vol.3
, Issue.4
, pp. 413-421
-
-
Jenkins, J.L.1
Bender, A.2
Davies, J.W.3
-
6
-
-
84870026354
-
Rules for identifying potentially reactive or promiscuous compounds
-
Bruns, R. F., and Watson, I. A. (2012) Rules for identifying potentially reactive or promiscuous compounds. J. Med. Chem. 55(22), 9763-9772.
-
(2012)
J. Med. Chem.
, vol.55
, Issue.22
, pp. 9763-9772
-
-
Bruns, R.F.1
Watson, I.A.2
-
7
-
-
84941595522
-
An aggregation advisor for ligand discovery
-
Irwin, J. J., Duan, D., Torosyan, H., Doak, A. K., Ziebart, K. T., Sterling, T., Tumanian, G., and Shoichet, B. K. (2015) An Aggregation Advisor for Ligand Discovery. J. Med. Chem. 58(17), 7076-7087.
-
(2015)
J. Med. Chem.
, vol.58
, Issue.17
, pp. 7076-7087
-
-
Irwin, J.J.1
Duan, D.2
Torosyan, H.3
Doak, A.K.4
Ziebart, K.T.5
Sterling, T.6
Tumanian, G.7
Shoichet, B.K.8
-
8
-
-
84867443730
-
Mining collections of compounds with Screening Assistant 2
-
Guilloux, V., Arrault, A., Colliandre, L., Bourg, S., Vayer, P., and Morin-Allory, L. (2012) Mining collections of compounds with Screening Assistant 2. J. Cheminf. 4(1), 20.
-
(2012)
J. Cheminf.
, vol.4
, Issue.1
, pp. 20
-
-
Guilloux, V.1
Arrault, A.2
Colliandre, L.3
Bourg, S.4
Vayer, P.5
Morin-Allory, L.6
-
9
-
-
84995511489
-
Analyzing promiscuity at the level of active compounds and targets
-
Bajorath, J. (2016) Analyzing Promiscuity at the Level of Active Compounds and Targets. Mol. Inf., DOI: 10.1002/minf.201600030.
-
(2016)
Mol. Inf..
-
-
Bajorath, J.1
-
10
-
-
33644876210
-
DrugBank: A comprehensive resource for in silico drug discovery and exploration
-
Wishart, D. S., Knox, C., Guo, A. C., Shrivastava, S., Hassanali, M., Stothard, P., Chang, Z., and Woolsey, J. (2006) DrugBank: A comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 34, D668-D672.
-
(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
-
11
-
-
84891767304
-
DrugBank 4.0: Shedding new light on drug metabolism
-
Law, V., Knox, C., Djoumbou, Y., Jewison, T., Guo, A. C., Liu, Y., Maciejewski, A., Arndt, D., Wilson, M., Neveu, V., Tang, A., Gabriel, G., Ly, C., Adamjee, S., Dame, Z. T., Han, B., Zhou, Y., and Wishart, D. S. (2014) DrugBank 4.0: Shedding new light on drug metabolism. Nucleic Acids Res. 42(D1), D1091-D1097.
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.D1
, pp. D1091-D1097
-
-
Law, V.1
Knox, C.2
Djoumbou, Y.3
Jewison, T.4
Guo, A.C.5
Liu, Y.6
Maciejewski, A.7
Arndt, D.8
Wilson, M.9
Neveu, V.10
Tang, A.11
Gabriel, G.12
Ly, C.13
Adamjee, S.14
Dame, Z.T.15
Han, B.16
Zhou, Y.17
Wishart, D.S.18
-
12
-
-
84976907502
-
KEGG as a reference resource for gene and protein annotation
-
Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M. (2016) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44(D1), D457-D462.
-
(2016)
Nucleic Acids Res
, vol.44
, Issue.D1
, pp. D457-D462
-
-
Kanehisa, M.1
Sato, Y.2
Kawashima, M.3
Furumichi, M.4
Tanabe, M.5
-
13
-
-
84891762026
-
The ChEMBL bioactivity database: An update
-
Bento, A. P., Gaulton, A., Hersey, A., Bellis, L. J., Chambers, J., Davies, M., Kruger, F. A., Light, Y., Mak, L., McGlinchey, S., Nowotka, M., Papadatos, G., Santos, R., and Overington, J. P. (2014) The ChEMBL bioactivity database: An update. Nucleic Acids Res. 42(D1), D1083-D1090.
-
(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
Kruger, 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
-
14
-
-
84979586933
-
PubChem Substance and Compound databases
-
Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., Wang, J., Yu, B., Zhang, J., and Bryant, S. H. (2016) PubChem Substance and Compound databases. Nucleic Acids Res. 44(D1), D1202-13.
-
(2016)
Nucleic Acids Res
, vol.44
, Issue.D1
, pp. D1202-D1213
-
-
Kim, S.1
Thiessen, P.A.2
Bolton, E.E.3
Chen, J.4
Fu, G.5
Gindulyte, A.6
Han, L.7
He, J.8
He, S.9
Shoemaker, B.A.10
Wang, J.11
Yu, B.12
Zhang, J.13
Bryant, S.H.14
-
15
-
-
84891805328
-
PubChem BioAssay: 2014 update
-
Wang, Y., Suzek, T., Zhang, J., Wang, J., He, S., Cheng, T., Shoemaker, B. A., Gindulyte, A., and Bryant, S. H. (2014) PubChem BioAssay: 2014 update. Nucleic Acids Res. 42, D1075-82.
-
(2014)
Nucleic Acids Res
, vol.42
, 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
-
16
-
-
85035040042
-
-
accessed August 5, 2016
-
WHO Collaborating Centre for Drug Statistics Methodology. http://www.whocc.no/atc/structure- and-principles/ (accessed August 5, 2016).
-
-
-
-
17
-
-
0035289779
-
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
-
Lipinski, C. A., Lombardo, F., Dominy, B. W., and Feeney, P. J. (1997) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Delivery Rev. 23(1-3), 3-25.
-
(1997)
Adv. Drug Delivery Rev.
, vol.23
, Issue.1-3
, pp. 3-25
-
-
Lipinski, C.A.1
Lombardo, F.2
Dominy, B.W.3
Feeney, P.J.4
-
18
-
-
84968923096
-
WOMBAT: World of Molecular Bioactivity
-
Oprea, T. I., Ed., Methods and Principles in Medicinal Chemistry, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany
-
Olah, M., Mracec, M., Ostopovici, L., Rad, R., Bora, A., Hadaruga, N., Olah, I., Banda, M., Simon, Z., Mracec, M., and Oprea, T. I. (2005) WOMBAT: World of Molecular Bioactivity, In Chemoinformatics in Drug Discovery (Oprea, T. I., Ed.), pp 221-239, Methods and Principles in Medicinal Chemistry, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany.
-
(2005)
Chemoinformatics in Drug Discovery
, pp. 221-239
-
-
Olah, M.1
Mracec, M.2
Ostopovici, L.3
Rad, R.4
Bora, A.5
Hadaruga, N.6
Olah, I.7
Banda, M.8
Simon, Z.9
Mracec, M.10
Oprea, T.I.11
-
19
-
-
84887054523
-
Estimating error rates in bioactivity databases
-
Tiikkainen, P., Bellis, L., Light, Y., and Franke, L. (2013) Estimating error rates in bioactivity databases. J. Chem. Inf. Model. 53(10), 2499-2505.
-
(2013)
J. Chem. Inf. Model.
, vol.53
, Issue.10
, pp. 2499-2505
-
-
Tiikkainen, P.1
Bellis, L.2
Light, Y.3
Franke, L.4
-
20
-
-
84976902303
-
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology
-
Gilson, M. K., Liu, T., Baitaluk, M., Nicola, G., Hwang, L., and Chong, J. (2016) BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Res. 44(D1), D1045-D1053.
-
(2016)
Nucleic Acids Res
, vol.44
, Issue.D1
, pp. D1045-D1053
-
-
Gilson, M.K.1
Liu, T.2
Baitaluk, M.3
Nicola, G.4
Hwang, L.5
Chong, J.6
-
21
-
-
0035658264
-
BindingDB: A Web-Accessible Molecular Recognition Database
-
Chen, X., Liu, M., and Gilson, M. (2001) BindingDB: A Web-Accessible Molecular Recognition Database. Comb. Chem. High Throughput Screening 4(8), 719-725.
-
(2001)
Comb. Chem. High Throughput Screening
, vol.4
, Issue.8
, pp. 719-725
-
-
Chen, X.1
Liu, M.2
Gilson, M.3
-
22
-
-
67849104638
-
PubChem: A public information system for analyzing bioactivities of small molecules
-
Wang, Y., Xiao, J., Suzek, T. O., Zhang, J., Wang, J., and Bryant, S. H. (2009) PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res. 37, W623-W633.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. W623-W633
-
-
Wang, Y.1
Xiao, J.2
Suzek, T.O.3
Zhang, J.4
Wang, J.5
Bryant, S.H.6
-
23
-
-
84868138829
-
Open PHACTS: Semantic interoperability for drug discovery
-
Williams, A. J., Harland, L., Groth, P., Pettifer, S., Chichester, C., Willighagen, E. L., Evelo, C. T., Blomberg, N., Ecker, G., Goble, C., and Mons, B. (2012) Open PHACTS: Semantic interoperability for drug discovery. Drug Discovery Today 17(21-22), 1188-1198.
-
(2012)
Drug Discovery Today
, vol.17
, Issue.21-22
, pp. 1188-1198
-
-
Williams, A.J.1
Harland, L.2
Groth, P.3
Pettifer, S.4
Chichester, C.5
Willighagen, E.L.6
Evelo, C.T.7
Blomberg, N.8
Ecker, G.9
Goble, C.10
Mons, B.11
-
24
-
-
84908353448
-
Applying linked data approaches to pharmacology: Architectural decisions and implementation
-
Gray, A. J. G., Groth, P., Loizou, A., Askjaer, S., Brenninkmeijer, C., Burger, K, Chichester, C., Evelo, C. T., Goble, C., Harland, L., Pettifer, S., Thompson, M., Waagmeester, A, and Williams, A. J. (2014) Applying Linked Data Approaches to Pharmacology: Architectural Decisions and Implementation. Semantic Web 5(2), 101-113.
-
(2014)
Semantic Web
, vol.5
, Issue.2
, pp. 101-113
-
-
Gray, A.J.G.1
Groth, P.2
Loizou, A.3
Askjaer, S.4
Brenninkmeijer, C.5
Burger, K.6
Chichester, C.7
Evelo, C.T.8
Goble, C.9
Harland, L.10
Pettifer, S.11
Thompson, M.12
Waagmeester, A.13
Williams, A.J.14
-
25
-
-
79251561193
-
TCM Database@ Taiwan: The World's Largest Traditional Chinese Medicine Database for Drug Screening in Silico
-
Chen, C. Y.-C., and Hofmann, A (2011) TCM Database@ Taiwan: The World's Largest Traditional Chinese Medicine Database for Drug Screening In Silico. PLoS One 6(1), e15939.
-
(2011)
PLoS One
, vol.6
, Issue.1
, pp. e15939
-
-
Chen, C.Y.-C.1
Hofmann, A.2
-
26
-
-
40549130652
-
PDTD: A web-accessible protein database for drug target identification
-
Gao, Z., Li, H., Zhang, H., Liu, X., Kang, L., Luo, X., Zhu, W., Chen, K, Wang, X., and Jiang, H. (2008) PDTD: a web-accessible protein database for drug target identification. BMC Bioinf. 9, 104.
-
(2008)
BMC Bioinf
, vol.9
, pp. 104
-
-
Gao, Z.1
Li, H.2
Zhang, H.3
Liu, X.4
Kang, L.5
Luo, X.6
Zhu, W.7
Chen, K.8
Wang, X.9
Jiang, H.10
-
27
-
-
84941103395
-
BRENDA in 2015: Exciting developments in its 25th year of existence
-
Chang, A, Schomburg, I., Placzek, S., Jeske, L., Ulbrich, M., Xiao, M., Sensen, C. W., and Schomburg, D. (2015) BRENDA in 2015: Exciting developments in its 25th year of existence. Nucleic Acids Res. 43(D1), D439-D446.
-
(2015)
Nucleic Acids Res
, vol.43
, Issue.D1
, pp. D439-D446
-
-
Chang, A.1
Schomburg, I.2
Placzek, S.3
Jeske, L.4
Ulbrich, M.5
Xiao, M.6
Sensen, C.W.7
Schomburg, D.8
-
28
-
-
2542530042
-
The PDBbind Database: Collection of Binding Affinities for Protein-Ligand Complexes with Known Three-Dimensional Structures: Collection of Binding Affinities for Protein-Ligand Complexes with Known Three-Dimensional Structures
-
Wang, R., Fang, X., Lu, Y., and Wang, S. (2004) The PDBbind Database: Collection of Binding Affinities for Protein-Ligand Complexes with Known Three-Dimensional Structures: Collection of Binding Affinities for Protein-Ligand Complexes with Known Three-Dimensional Structures. J. Med. Chem. 47(12), 2977-2980.
-
(2004)
J. Med. Chem.
, vol.47
, Issue.12
, pp. 2977-2980
-
-
Wang, R.1
Fang, X.2
Lu, Y.3
Wang, S.4
-
29
-
-
20444422149
-
The PDBbind Database: Methodologies and Updates
-
Wang, R., Fang, X., Lu, Y., Yang, C.-Y., and Wang, S. (2005) The PDBbind Database: Methodologies and Updates. J. Med. Chem. 48(12), 4111-4119.
-
(2005)
J. Med. Chem.
, vol.48
, Issue.12
, pp. 4111-4119
-
-
Wang, R.1
Fang, X.2
Lu, Y.3
Yang, C.-Y.4
Wang, S.5
-
30
-
-
84976870113
-
The reactome pathway knowledgebase
-
Fabregat, A., Sidiropoulos, K, Garapati, P., Gillespie, M., Hausmann, K, Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S., Matthews, L., May, B., Mlacic, M., Rothfels, K, Shamovsky, V., Webber, M., Weiser, J., Williams, M., Wu, G., Stein, L., Hermjakob, H., and D'Eustachio, P. (2016) The Reactome pathway Knowledgebase. Nucleic Acids Res. 44(D1), D481-7.
-
(2016)
Nucleic Acids Res
, vol.44
, Issue.D1
, pp. D481-D487
-
-
Fabregat, A.1
Sidiropoulos, K.2
Garapati, P.3
Gillespie, M.4
Hausmann, K.5
Haw, R.6
Jassal, B.7
Jupe, S.8
Korninger, F.9
McKay, S.10
Matthews, L.11
May, B.12
Mlacic, M.13
Rothfels, K.14
Shamovsky, V.15
Webber, M.16
Weiser, J.17
Williams, M.18
Wu, G.19
Stein, L.20
Hermjakob, H.21
D'Eustachio, P.22
more..
-
31
-
-
84976868788
-
WikiPathways: Capturing the full diversity of pathway knowledge
-
Kutmon, M., Riutta, A., Nunes, N, Hanspers, K, Willighagen, E. L., Bohler, A., Melius, J., Waagmeester, A, Sinha, S. R., Miller, R., Coort, S. L., Cirillo, E., Smeets, B., Evelo, C. T., and Pico, A. R (2016) WikiPathways: capturing the full diversity of pathway knowledge. Nucleic Acids Res. 44(D1), D488-94.
-
(2016)
Nucleic Acids Res
, vol.44
, Issue.D1
, pp. D488-D494
-
-
Kutmon, M.1
Riutta, A.2
Nunes, N.3
Hanspers, K.4
Willighagen, E.L.5
Bohler, A.6
Melius, J.7
Waagmeester, A.8
Sinha, S.R.9
Miller, R.10
Coort, S.L.11
Cirillo, E.12
Smeets, B.13
Evelo, C.T.14
Pico, A.R.15
-
32
-
-
13844312649
-
ZINC-a free database of commercially available compounds for virtual screening
-
Irwin, J. J., and Shoichet, B. K (2005) ZINC-a free database of commercially available compounds for virtual screening. J. Chem. Inf. Model. 45(1), 177-182.
-
(2005)
J. Chem. Inf. Model.
, vol.45
, Issue.1
, pp. 177-182
-
-
Irwin, J.J.1
Shoichet, B.K.2
-
33
-
-
84864199587
-
ZINC: A free tool to discover chemistry for biology
-
Irwin, J. J., Sterling, T., Mysinger, M. M., Bolstad, E. S., and Coleman, R. G (2012) ZINC: a free tool to discover chemistry for biology. J. Chem. Inf. Model. 52(7), 1757-1768.
-
(2012)
J. Chem. Inf. Model.
, vol.52
, Issue.7
, pp. 1757-1768
-
-
Irwin, J.J.1
Sterling, T.2
Mysinger, M.M.3
Bolstad, E.S.4
Coleman, R.G.5
-
34
-
-
38549127678
-
ChEBI: A database and ontology for chemical entities of biological interest
-
Database
-
Degtyarenko, K, de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcantara, R., Darsow, M., Guedj, M., and Ashburner, M. (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36 (Database), D344-50.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. D344-D350
-
-
Degtyarenko, K.1
De Matos, P.2
Ennis, M.3
Hastings, J.4
Zbinden, M.5
McNaught, A.6
Alcantara, R.7
Darsow, M.8
Guedj, M.9
Ashburner, M.10
-
35
-
-
84876560358
-
The ChEBI reference database and ontology for biologically relevant chemistry: Enhancements for 2013
-
Hastings, J., de Matos, P., Dekker, A, Ennis, M., Harsha, B., Kale, N, Muthukrishnan, V., Owen, G, Turner, S., Williams, M., and Steinbeck, C. (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res. 41(D1), D456-D463.
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.D1
, pp. D456-D463
-
-
Hastings, J.1
De Matos, P.2
Dekker, A.3
Ennis, M.4
Harsha, B.5
Kale, N.6
Muthukrishnan, V.7
Owen, G.8
Turner, S.9
Williams, M.10
Steinbeck, C.11
-
36
-
-
84948442908
-
ZINC 15-Ligand Discovery for Everyone
-
Sterling, T., and Irwin, J. J. (2015) ZINC 15-Ligand Discovery for Everyone. J. Chem. Inf. Model. 55(11), 2324-2337.
-
(2015)
J. Chem. Inf. Model.
, vol.55
, Issue.11
, pp. 2324-2337
-
-
Sterling, T.1
Irwin, J.J.2
-
37
-
-
84937680248
-
Editorial: ChemSpider-A Tool for Natural Products Research
-
(2015) Editorial: ChemSpider-A Tool for Natural Products Research. Nat. Prod. Rep. 32(8), 1163-1164. DOI: 10.1039/C5NP90022K
-
(2015)
Nat. Prod. Rep.
, vol.32
, Issue.8
, pp. 1163-1164
-
-
-
38
-
-
75549092202
-
Chemical entities of biological interest: An update
-
Database
-
de Matos, P., Alcantara, R., Dekker, A., Ennis, M., Hastings, J., Haug, K, Spiteri, I., Turner, S., and Steinbeck, C. (2010) Chemical Entities of Biological Interest: an update. Nucleic Acids Res. 38 (Database), D249-D254.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. D249-D254
-
-
De Matos, P.1
Alcantara, R.2
Dekker, A.3
Ennis, M.4
Hastings, J.5
Haug, K.6
Spiteri, I.7
Turner, S.8
Steinbeck, C.9
-
39
-
-
0037119336
-
From protein domains to drug candidates-natural products as guiding principles in the design and synthesis of compound libraries
-
Breinbauer, R., Vetter, I. R., and Waldmann, H. (2002) From Protein Domains to Drug Candidates-Natural Products as Guiding Principles in the Design and Synthesis of Compound Libraries. Angew. Chem., Int. Ed. 41(16), 2878.
-
(2002)
Angew. Chem., Int. Ed.
, vol.41
, Issue.16
, pp. 2878
-
-
Breinbauer, R.1
Vetter, I.R.2
Waldmann, H.3
-
40
-
-
84866355546
-
Exploring chemical space for drug discovery using the chemical universe database
-
Reymond, J.-L., and Awale, M. (2012) Exploring chemical space for drug discovery using the chemical universe database. ACS Chem. Neurosci. 3(9), 649-657.
-
(2012)
ACS Chem. Neurosci.
, vol.3
, Issue.9
, pp. 649-657
-
-
Reymond, J.-L.1
Awale, M.2
-
41
-
-
84869987352
-
Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17
-
Ruddigkeit, L., van Deursen, R., Blum, L. C., and Reymond, J.-L. (2012) Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17. J. Chem. Inf. Model. 52(11), 2864-2875.
-
(2012)
J. Chem. Inf. Model.
, vol.52
, Issue.11
, pp. 2864-2875
-
-
Ruddigkeit, L.1
Van Deursen, R.2
Blum, L.C.3
Reymond, J.-L.4
-
42
-
-
0001752768
-
The Cambridge Structural Database: A quarter of a million crystal structures and rising
-
Allen, F. H. (2002) The Cambridge Structural Database: A quarter of a million crystal structures and rising. Acta Crystallogr., Sect. B: Struct. Sci. 58(3), 380-388.
-
(2002)
Acta Crystallogr., Sect. B: Struct. Sci.
, vol.58
, Issue.3
, pp. 380-388
-
-
Allen, F.H.1
-
43
-
-
84923328756
-
DataWarrior: An Open-Source Program for Chemistry Aware Data Visualization and Analysis
-
Sander, T., Freyss, J., von Korff, M., and Rufener, C. (2015) DataWarrior: An Open-Source Program For Chemistry Aware Data Visualization And Analysis. J. Chem. Inf. Model. 55(2), 460-473.
-
(2015)
J. Chem. Inf. Model.
, vol.55
, Issue.2
, pp. 460-473
-
-
Sander, T.1
Freyss, J.2
Von Korff, M.3
Rufener, C.4
-
44
-
-
84856782646
-
Nonlinear dimensionality reduction and mapping of compound libraries for drug discovery
-
Reutlinger, M., and Schneider, G. (2012) Nonlinear dimensionality reduction and mapping of compound libraries for drug discovery. J. Mol. Graphics Modell. 34, 108-117.
-
(2012)
J. Mol. Graphics Modell.
, vol.34
, pp. 108-117
-
-
Reutlinger, M.1
Schneider, G.2
-
45
-
-
42149090634
-
Structure-activity landscape index: Identifying and quantifying activity cliffs
-
Guha, R., and van Drie, J. H. (2008) Structure-activity landscape index: identifying and quantifying activity cliffs. J. Chem. Inf. Model. 48(3), 646-658.
-
(2008)
J. Chem. Inf. Model.
, vol.48
, Issue.3
, pp. 646-658
-
-
Guha, R.1
Van Drie, J.H.2
-
46
-
-
84887113038
-
MONA - Interactive manipulation of molecule collections
-
Hilbig, M., Urbaczek, S., Groth, I., Heuser, S., and Rarey, M. (2013) MONA - Interactive manipulation of molecule collections. J. Cheminf. 5(1), 38.
-
(2013)
J. Cheminf.
, vol.5
, Issue.1
, pp. 38
-
-
Hilbig, M.1
Urbaczek, S.2
Groth, I.3
Heuser, S.4
Rarey, M.5
-
47
-
-
84945547307
-
MONA 2: A Light Cheminformatics Platform for Interactive Compound Library Processing
-
Hilbig, M., and Rarey, M. (2015) MONA 2: A Light Cheminformatics Platform for Interactive Compound Library Processing. J. Chem. Inf. Model. 55(10), 2071-2078.
-
(2015)
J. Chem. Inf. Model.
, vol.55
, Issue.10
, pp. 2071-2078
-
-
Hilbig, M.1
Rarey, M.2
-
48
-
-
84908530414
-
Chemistry: Chemical con artists foil drug discovery
-
Baell, J., and Walters, M. A. (2014) Chemistry: Chemical con artists foil drug discovery. Nature 513(7519), 481-483.
-
(2014)
Nature
, vol.513
, Issue.7519
, pp. 481-483
-
-
Baell, J.1
Walters, M.A.2
-
49
-
-
84891895456
-
PAINS: Relevance to Tool Compound Discovery and Fragment-Based Screening
-
Baell, J. B., Ferrins, L., Falk, H., and Nikolakopoulos, G. (2013) PAINS: Relevance to Tool Compound Discovery and Fragment-Based Screening. Aust. J. Chem. 66(12), 1483.
-
(2013)
Aust. J. Chem.
, vol.66
, Issue.12
, pp. 1483
-
-
Baell, J.B.1
Ferrins, L.2
Falk, H.3
Nikolakopoulos, G.4
-
50
-
-
33846871027
-
The scaffold tree-visualization of the scaffold universe by hierarchical scaffold classification
-
Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A., and Waldmann, H. (2007) The Scaffold Tree-Visualization of the Scaffold Universe by Hierarchical Scaffold Classification. J. Chem. Inf. Model. 47(1), 47-58.
-
(2007)
J. Chem. Inf. Model.
, vol.47
, Issue.1
, pp. 47-58
-
-
Schuffenhauer, A.1
Ertl, P.2
Roggo, S.3
Wetzel, S.4
Koch, M.A.5
Waldmann, H.6
-
51
-
-
84894553454
-
Visual analysis of biological activity data with scaffold hunter
-
Klein, K., Koch, O., Kriege, N., Mutzel, P., and Schafer, T. (2013) Visual Analysis of Biological Activity Data with Scaffold Hunter. Mol. Inf. 32(11-12), 964-975.
-
(2013)
Mol. Inf.
, vol.32
, Issue.11-12
, pp. 964-975
-
-
Klein, K.1
Koch, O.2
Kriege, N.3
Mutzel, P.4
Schafer, T.5
-
52
-
-
68049098031
-
Interactive exploration of chemical space with Scaffold Hunter
-
Wetzel, S., Klein, K., Renner, S., Rauh, D., Oprea, T. I., Mutzel, P., and Waldmann, H. (2009) Interactive exploration of chemical space with Scaffold Hunter. Nat. Chem. Biol. 5(8), 581-583.
-
(2009)
Nat. Chem. Biol.
, vol.5
, Issue.8
, pp. 581-583
-
-
Wetzel, S.1
Klein, K.2
Renner, S.3
Rauh, D.4
Oprea, T.I.5
Mutzel, P.6
Waldmann, H.7
-
53
-
-
84904620383
-
Scaffold hunter: Facilitating drug discovery by visual analysis of chemical space, in computer vision, imaging and computer graphics
-
Csurka, G., Kraus, M., Laramee, R. S., Richard, P., and Braz, J., Eds., Communications in Computer and Information Science, Springer, Berlin
-
Klein, K., Kriege, N., and Mutzel, P. (2013) Scaffold Hunter: Facilitating Drug Discovery by Visual Analysis of Chemical Space, In Computer Vision, Imaging and Computer Graphics. Theory and Application (Csurka, G., Kraus, M., Laramee, R. S., Richard, P., and Braz, J., Eds.), pp 176-192, Communications in Computer and Information Science, Springer, Berlin.
-
(2013)
Theory and Application
, pp. 176-192
-
-
Klein, K.1
Kriege, N.2
Mutzel, P.3
-
54
-
-
84921832778
-
Practical SAHN Clustering for Very Large Data Sets and Expensive Distance Metrics
-
Kriege, N., Mutzel, P., and Schafer, T. (2014) Practical SAHN Clustering for Very Large Data Sets and Expensive Distance Metrics. J. Graph Algorithms Appl. 18(4), 577-602.
-
(2014)
J. Graph Algorithms Appl.
, vol.18
, Issue.4
, pp. 577-602
-
-
Kriege, N.1
Mutzel, P.2
Schafer, T.3
-
55
-
-
84879557098
-
KNIME: The Konstanz Information Miner
-
March 7-9, Preisach, C., Ed., Studies in Classification, Data Analysis, and Knowledge Organization 31, Springer, Berlin
-
Berthold, M. R., Cebron, N., Dill, F., Gabriel, T. R., Kotter, T., Meinl, T., Ohl, P., Sieb, C., Thiel, K., and Wiswedel, B. (2008) KNIME: The Konstanz Information Miner, In Data Analysis, Machine Learning and Applications: Albert-Ludwigs-Universitat Freiburg, March 7-9, 2007 (Preisach, C., Ed.), Studies in Classification, Data Analysis, and Knowledge Organization 31, Springer, Berlin.
-
(2007)
Data Analysis, Machine Learning and Applications: Albert-ludwigs-universitat Freiburg
-
-
Berthold, M.R.1
Cebron, N.2
Dill, F.3
Gabriel, T.R.4
Kotter, T.5
Meinl, T.6
Ohl, P.7
Sieb, C.8
Thiel, K.9
Wiswedel, B.10
-
56
-
-
78651076564
-
KNIME - The Konstanz information miner
-
Berthold, M. R., Cebron, N., Dill, F., Gabriel, T. R., Kotter, T., Meinl, T., Ohl, P., Thiel, K., and Wiswedel, B. (2009) KNIME - the Konstanz information miner. SIGKDD Explor. Newsl. 11(1), 26.
-
(2009)
SIGKDD Explor. Newsl
, vol.11
, Issue.1
, pp. 26
-
-
Berthold, M.R.1
Cebron, N.2
Dill, F.3
Gabriel, T.R.4
Kotter, T.5
Meinl, T.6
Ohl, P.7
Thiel, K.8
Wiswedel, B.9
-
57
-
-
84870022937
-
Similarity coefficients for binary chemoinformatics data: Overview and extended comparison using simulated and real data sets
-
Todeschini, R., Consonni, V., Xiang, H., Holliday, J., Buscema, M., and Willett, P. (2012) Similarity coefficients for binary chemoinformatics data: overview and extended comparison using simulated and real data sets. J. Chem. Inf. Model. 52(11), 2884-2901.
-
(2012)
J. Chem. Inf. Model.
, vol.52
, Issue.11
, pp. 2884-2901
-
-
Todeschini, R.1
Consonni, V.2
Xiang, H.3
Holliday, J.4
Buscema, M.5
Willett, P.6
-
58
-
-
84882310107
-
The taverna workflow suite: Designing and executing workflows of web services on the desktop, web or in the cloud
-
Wolstencroft, K., Haines, R., Fellows, D., Williams, A., Withers, D., Owen, S., Soiland-Reyes, S., Dunlop, I., Nenadic, A., Fisher, P., Bhagat, J., Belhajjame, K., Bacall, F., Hardisty, A., Nieva de la Hidalga, A., Balcazar Vargas, M. P., Sufi, S., and Goble, C. (2013) The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud. Nucleic Acids Res. 41(W1), W557-W561.
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.W1
, pp. W557-W561
-
-
Wolstencroft, K.1
Haines, R.2
Fellows, D.3
Williams, A.4
Withers, D.5
Owen, S.6
Soiland-Reyes, S.7
Dunlop, I.8
Nenadic, A.9
Fisher, P.10
Bhagat, J.11
Belhajjame, K.12
Bacall, F.13
Hardisty, A.14
Nieva De La Hidalga, A.15
Balcazar Vargas, M.P.16
Sufi, S.17
Goble, C.18
-
59
-
-
84911496459
-
Revealing the macromolecular targets of complex natural products
-
Reker, D., Perna, A. M., Rodrigues, T., Schneider, P., Reutlinger, M., Monch, B., Koeberle, A., Lamers, C., Gabler, M., Steinmetz, H., Muller, R., Schubert-Zsilavecz, M., Werz, O., and Schneider, G. (2014) Revealing the macromolecular targets of complex natural products. Nat. Chem. 6(12), 1072-1078.
-
(2014)
Nat. Chem.
, vol.6
, Issue.12
, pp. 1072-1078
-
-
Reker, D.1
Perna, A.M.2
Rodrigues, T.3
Schneider, P.4
Reutlinger, M.5
Monch, B.6
Koeberle, A.7
Lamers, C.8
Gabler, M.9
Steinmetz, H.10
Muller, R.11
Schubert-Zsilavecz, M.12
Werz, O.13
Schneider, G.14
-
60
-
-
84896525962
-
Identifying the macromolecular targets of de novo-designed chemical entities through self-organizing map consensus
-
Reker, D., Rodrigues, T., Schneider, P., and Schneider, G. (2014) Identifying the macromolecular targets of de novo-designed chemical entities through self-organizing map consensus. Proc. Natl. Acad. Sci. U. S. A. 111(11), 4067-4072.
-
(2014)
Proc. Natl. Acad. Sci. U. S. A.
, vol.111
, Issue.11
, pp. 4067-4072
-
-
Reker, D.1
Rodrigues, T.2
Schneider, P.3
Schneider, G.4
-
61
-
-
84904821175
-
SuperPred: Update on drug classification and target prediction
-
Nickel, J., Gohlke, B.-O., Erehman, J., Banerjee, P., Rong, W. W., Goede, A., Dunkel, M., and Preissner, R. (2014) SuperPred: update on drug classification and target prediction. Nucleic Acids Res. 42(W1), W26-W31.
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.W1
, pp. W26-W31
-
-
Nickel, J.1
Gohlke, B.-O.2
Erehman, J.3
Banerjee, P.4
Rong, W.W.5
Goede, A.6
Dunkel, M.7
Preissner, R.8
-
62
-
-
84883143619
-
Igpcr-drug: A web server for predicting interaction between GPCRs and drugs in cellular networking
-
Xiao, X., Min, J.-L., Wang, P., and Chou, K.-C. (2013) iGPCR-drug: a web server for predicting interaction between GPCRs and drugs in cellular networking. PLoS One 8(8), e72234.
-
(2013)
PLoS One
, vol.8
, Issue.8
, pp. e72234
-
-
Xiao, X.1
Min, J.-L.2
Wang, P.3
Chou, K.-C.4
-
63
-
-
84904805614
-
DINIES: Drug-target interaction network inference engine based on supervised analysis
-
Yamanishi, Y., Kotera, M., Moriya, Y., Sawada, R., Kanehisa, M., and Goto, S. (2014) DINIES: drug-target interaction network inference engine based on supervised analysis. Nucleic Acids Res. 42(W1), W39-W45.
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.W1
, pp. W39-W45
-
-
Yamanishi, Y.1
Kotera, M.2
Moriya, Y.3
Sawada, R.4
Kanehisa, M.5
Goto, S.6
-
64
-
-
33846876695
-
Relating protein pharmacology by ligand chemistry
-
Keiser, M. J., Roth, B. L., Armbruster, B. N., Ernsberger, P., Irwin, J. J., and Shoichet, B. K. (2007) Relating protein pharmacology by ligand chemistry. Nat. Biotechnol. 25(2), 197-206.
-
(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
-
65
-
-
84885904434
-
The CARLSBAD database: A confederated database of chemical bioactivities
-
Mathias, S. L., Hines-Kay, J., Yang, J. J., Zahoransky-Kohalmi, G., Bologa, C. G., Ursu, O., and Oprea, T. I. (2013) The CARLSBAD database: a confederated database of chemical bioactivities. Database 2013, bat044.
-
(2013)
Database
, vol.2013
, pp. bat044
-
-
Mathias, S.L.1
Hines-Kay, J.2
Yang, J.J.3
Zahoransky-Kohalmi, G.4
Bologa, C.G.5
Ursu, O.6
Oprea, T.I.7
-
66
-
-
84908284638
-
-
ICH - International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use accessed August 5, 2016
-
ICH - International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use. M7 Assessment and Control of DNA Reactive (Mutagenic) Impurities in Pharmaceuticals to Limit Potential Carcinogenic Risk. http://www.ich.org/fileadmin/Public-Web-Site/ICH-Products/Guidelines/Multidisciplinary/M7/M7-Step-4.pdf (accessed August 5, 2016).
-
M7 Assessment and Control of DNA Reactive (Mutagenic) Impurities in Pharmaceuticals to Limit Potential Carcinogenic Risk
-
-
-
67
-
-
85034973380
-
-
accessed August 5, 2016
-
U. S. Food and Drug Administration. 1. Modernize Toxicology to Enhance Product Safety. http://www.fda.gov/ScienceResearch/SpecialTopics/RegulatoryScience/ucm268111.htm (accessed August 5, 2016).
-
Modernize Toxicology to Enhance Product Safety
-
-
-
68
-
-
79957469242
-
Collaborative development of predictive toxicology applications
-
Hardy, B., Douglas, N., Helma, C., Rautenberg, M., Jeliazkova, N., Jeliazkov, V., Nikolova, I., Benigni, R., Tcheremenskaia, O., Kramer, S., Girschick, T., Buchwald, F., Wicker, J., Karwath, A., Gutlein, M., Maunz, A., Sarimveis, H., Melagraki, G., Afantitis, A., Sopasakis, P., Gallagher, D., Poroikov, V., Filimonov, D., Zakharov, A., Lagunin, A., Gloriozova, T., Novikov, S., Skvortsova, N., Druzhilovsky, D., Chawla, S., Ghosh, I., Ray, S., Patel, H., and Escher, S. (2010) Collaborative development of predictive toxicology applications. J. Cheminf. 2(1), 7.
-
(2010)
J. Cheminf.
, vol.2
, Issue.1
, pp. 7
-
-
Hardy, B.1
Douglas, N.2
Helma, C.3
Rautenberg, M.4
Jeliazkova, N.5
Jeliazkov, V.6
Nikolova, I.7
Benigni, R.8
Tcheremenskaia, O.9
Kramer, S.10
Girschick, T.11
Buchwald, F.12
Wicker, J.13
Karwath, A.14
Gutlein, M.15
Maunz, A.16
Sarimveis, H.17
Melagraki, G.18
Afantitis, A.19
Sopasakis, P.20
Gallagher, D.21
Poroikov, V.22
Filimonov, D.23
Zakharov, A.24
Lagunin, A.25
Gloriozova, T.26
Novikov, S.27
Skvortsova, N.28
Druzhilovsky, D.29
Chawla, S.30
Ghosh, I.31
Ray, S.32
Patel, H.33
Escher, S.34
more..
-
69
-
-
85007557350
-
Badapple: Promiscuity patterns from noisy evidence
-
Yang, J. J., Ursu, O., Lipinski, C. A., Sklar, L. A., Oprea, T. I., and Bologa, C. G. (2016) Badapple: promiscuity patterns from noisy evidence. J. Cheminf. 8, 29.
-
(2016)
J. Cheminf.
, vol.8
, pp. 29
-
-
Yang, J.J.1
Ursu, O.2
Lipinski, C.A.3
Sklar, L.A.4
Oprea, T.I.5
Bologa, C.G.6
|