title: ChemProt-2.0: visual navigation in a disease chemical biology database.
abstract: ChemProt-2.0 (http://www.cbs.dtu.dk/services/ChemProt-2.0) is a public available compilation of multiple chemical-protein annotation resources integrated with diseases and clinical outcomes information. The database has been updated to >1.15 million compounds with 5.32 millions bioactivity measurements for 15 290 proteins. Each protein is linked to quality-scored human protein-protein interactions data based on more than half a million interactions, for studying diseases and biological outcomes (diseases, pathways and GO terms) through protein complexes. In ChemProt-2.0, therapeutic effects as well as adverse drug reactions have been integrated allowing for suggesting proteins associated to clinical outcomes. New chemical structure fingerprints were computed based on the similarity ensemble approach. Protein sequence similarity search was also integrated to evaluate the promiscuity of proteins, which can help in the prediction of off-target effects. Finally, the database was integrated into a visual interface that enables navigation of the pharmacological space for small molecules. Filtering options were included in order to facilitate and to guide dynamic search of specific queries.
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark.
authors.forename: Sonny
authors.initials: S
authors.lastname: Kim Kjærulff
authors.forename: Louis
authors.initials: L
authors.lastname: Wich
authors.forename: Jens
authors.initials: J
authors.lastname: Kringelum
authors.forename: Ulrik P
authors.initials: UP
authors.lastname: Jacobsen
authors.forename: Irene
authors.initials: I
authors.lastname: Kouskoumvekaki
authors.forename: Karine
authors.initials: K
authors.lastname: Audouze
authors.forename: Ole
authors.initials: O
authors.lastname: Lund
authors.forename: Søren
authors.initials: S
authors.lastname: Brunak
authors.forename: Tudor I
authors.initials: TI
authors.lastname: Oprea
authors.forename: Olivier
authors.initials: O
authors.lastname: Taboureau
mesh_terms: D003196:Computer Graphics; D062126:Databases, Chemical; D004194:Disease; D004358:Drug Therapy; D064420:Drug-Related Side Effects and Adverse Reactions; D006801:Humans; D020407:Internet; D004364:Pharmaceutical Preparations / Q000737:chemistry*; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry / Q000187:drug effects*; D020539:Sequence Analysis, Protein; D014584:User-Computer Interface
chemical_list: D004364:Pharmaceutical Preparations; D011506:Proteins