The ChEMBL bioactivity database: an update

ChEMBL is an open large-scale bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012 Nucleic Acids Research Database Issue. Since then, a variety of new data sources and improvements in functionality have contributed to the growth and utility of the resource. In particular, more comprehensive tracking of compounds from research stages through clinical development to market is provided through the inclusion of data from United States Adopted Name applications; a new richer data model for representing drug targets has been developed; and a number of methods have been put in place to allow users to more easily identify reliable data. Finally, access to ChEMBL is now available via a new Resource Description Framework format, in addition to the web-based interface, data downloads and web services.

[1]  Carolyn A. Fleeger,et al.  USP dictionary of USAN and international drug names , 1994 .

[2]  R. Guha,et al.  Profile of the GSK Published Protein Kinase Inhibitor Set Across ATP-Dependent and-Independent Luciferases: Implications for Reporter-Gene Assays , 2013, PloS one.

[3]  A. Vulpetti,et al.  The experimental uncertainty of heterogeneous public K(i) data. , 2012, Journal of medicinal chemistry.

[4]  Martin Augustin,et al.  A broad activity screen in support of a chemogenomic map for kinase signalling research and drug discovery. , 2013, The Biochemical journal.

[5]  Olivier Michielin,et al.  SwissBioisostere: a database of molecular replacements for ligand design , 2012, Nucleic Acids Res..

[6]  Alan Wise,et al.  Identification of small molecule agonists of the motilin receptor. , 2008, Bioorganic & medicinal chemistry letters.

[7]  Maria F. Sassano,et al.  Automated design of ligands to polypharmacological profiles , 2012, Nature.

[8]  F. Lombardo,et al.  Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. , 2001, Advanced drug delivery reviews.

[9]  Paul N. Schofield,et al.  The Units Ontology: a tool for integrating units of measurement in science , 2012, Database J. Biol. Databases Curation.

[10]  H. Yamada,et al.  The Japanese toxicogenomics project: application of toxicogenomics. , 2010, Molecular nutrition & food research.

[11]  Dietrich Rebholz-Schuhmann,et al.  UKPMC: a full text article resource for the life sciences , 2011, Nucleic Acids Res..

[12]  Simon Townson,et al.  Integrated Dataset of Screening Hits against Multiple Neglected Disease Pathogens , 2011, PLoS neglected tropical diseases.

[13]  John P. Overington,et al.  ChEMBL: a large-scale bioactivity database for drug discovery , 2011, Nucleic Acids Res..

[14]  Robert Petryszak,et al.  UniChem: a unified chemical structure cross-referencing and identifier tracking system , 2013, Journal of Cheminformatics.

[15]  María Martín,et al.  Activities at the Universal Protein Resource (UniProt) , 2013, Nucleic Acids Res..

[16]  P. Leeson,et al.  The influence of drug-like concepts on decision-making in medicinal chemistry , 2007, Nature Reviews Drug Discovery.

[17]  Michael J. Keiser,et al.  Large Scale Prediction and Testing of Drug Activity on Side-Effect Targets , 2012, Nature.

[18]  Miguel Prudêncio,et al.  Liver-stage malaria parasites vulnerable to diverse chemical scaffolds , 2012, Proceedings of the National Academy of Sciences.

[19]  Ubbo Visser,et al.  BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results , 2011, BMC Bioinformatics.

[20]  James Bailey,et al.  Document clustering of scientific texts using citation contexts , 2010, Information Retrieval.

[21]  Evan Bolton,et al.  PubChem's BioAssay Database , 2011, Nucleic Acids Res..

[22]  The UniProt Consortium,et al.  Update on activities at the Universal Protein Resource (UniProt) in 2013 , 2012, Nucleic Acids Res..

[23]  M. Congreve,et al.  A 'rule of three' for fragment-based lead discovery? , 2003, Drug discovery today.

[24]  Peter Ertl,et al.  JSME: a free molecule editor in JavaScript , 2013, Journal of Cheminformatics.

[25]  Jeremy N. Burrows,et al.  The Open Access Malaria Box: A Drug Discovery Catalyst for Neglected Diseases , 2013, PloS one.

[26]  David S. Roos,et al.  TDR Targets: a chemogenomics resource for neglected diseases , 2011, Nucleic Acids Res..

[27]  J. T. Metz,et al.  Ligand efficiency indices as guideposts for drug discovery. , 2005, Drug discovery today.

[28]  Brendan J. Frey,et al.  Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data , 2012, BMC Bioinformatics.

[29]  John P. Overington,et al.  Mapping small molecule binding data to structural domains , 2012, BMC Bioinformatics.

[30]  Organización Mundial de la Salud.  Guidelines for ATC classification and DDD assignment , 1996 .

[31]  N. Ozawa,et al.  Transporter Database, TP-Search: A Web-Accessible Comprehensive Database for Research in Pharmacokinetics of Drugs , 2004, Pharmaceutical Research.

[32]  Takuji Yoshida,et al.  Novel 16-membered macrolides modified at C-12 and C-13 positions of midecamycin A1 and miokamycin. Part 1: Synthesis and evaluation of 12,13-carbamate and 12-arylalkylamino-13-hydroxy analogues. , 2008, Bioorganic & medicinal chemistry.

[33]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[34]  Alfonso Mendoza,et al.  Fueling Open-Source Drug Discovery: 177 Small-Molecule Leads against Tuberculosis , 2013, ChemMedChem.

[35]  A. Hopkins,et al.  Ligand efficiency: a useful metric for lead selection. , 2004, Drug discovery today.

[36]  Jackie S. Scott,et al.  Potent achiral agonists of the ghrelin (growth hormone secretagogue) receptor. Part I: Lead identification. , 2007, Bioorganic & medicinal chemistry letters.

[37]  C. Steinbeck,et al.  The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web , 2011, PloS one.

[38]  G. V. Paolini,et al.  Quantifying the chemical beauty of drugs. , 2012, Nature chemistry.

[39]  Barend Mons,et al.  Open PHACTS: semantic interoperability for drug discovery. , 2012, Drug discovery today.

[40]  Bissan Al-Lazikani,et al.  canSAR: an integrated cancer public translational research and drug discovery resource , 2011, Nucleic Acids Res..

[41]  John M. Barnard,et al.  Chemical Similarity Searching , 1998, J. Chem. Inf. Comput. Sci..

[42]  Jürgen Bajorath,et al.  Extending the Activity Cliff Concept: Structural Categorization of Activity Cliffs and Systematic Identification of Different Types of Cliffs in the ChEMBL Database , 2012, J. Chem. Inf. Model..