ChemProt-2.0: visual navigation in a disease chemical biology database
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ChemProt-2.0 : visual navigation in a disease chemical biology database. / Kim Kjærulff, Sonny; Wich, Louis; Kringelum, Jens; Jacobsen, Ulrik P; Kouskoumvekaki, Irene; Audouze, Karine; Lund, Ole; Brunak, Søren; Oprea, Tudor I; Taboureau, Olivier.
In: Nucleic Acids Research, Vol. 41, No. Database issue, 01.2013, p. D464-9.Research output: Contribution to journal › Journal article › Research
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TY - JOUR
T1 - ChemProt-2.0
T2 - visual navigation in a disease chemical biology database
AU - Kim Kjærulff, Sonny
AU - Wich, Louis
AU - Kringelum, Jens
AU - Jacobsen, Ulrik P
AU - Kouskoumvekaki, Irene
AU - Audouze, Karine
AU - Lund, Ole
AU - Brunak, Søren
AU - Oprea, Tudor I
AU - Taboureau, Olivier
PY - 2013/1
Y1 - 2013/1
N2 - ChemProt-2.0 (https://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.
AB - ChemProt-2.0 (https://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.
KW - Computer Graphics
KW - Databases, Chemical
KW - Disease
KW - Drug Therapy
KW - Drug Toxicity
KW - Humans
KW - Internet
KW - Pharmaceutical Preparations
KW - Protein Interaction Mapping
KW - Proteins
KW - Sequence Analysis, Protein
KW - User-Computer Interface
U2 - 10.1093/nar/gks1166
DO - 10.1093/nar/gks1166
M3 - Journal article
C2 - 23185041
VL - 41
SP - D464-9
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - Database issue
ER -
ID: 68113913