STITCH 3: zooming in on protein-chemical interactions

TY - JOUR

T1 - STITCH 3

T2 - zooming in on protein-chemical interactions

AU - Kuhn, Michael

AU - Szklarczyk, Damian

AU - Franceschini, Andrea

AU - von Mering, Christian

AU - Jensen, Lars Juhl

AU - Bork, Peer

PY - 2012/1

Y1 - 2012/1

N2 - To facilitate the study of interactions between proteins and chemicals, we have created STITCH, an aggregated database of interactions connecting over 300,000 chemicals and 2.6 million proteins from 1133 organisms. Compared to the previous version, the number of chemicals with interactions and the number of high-confidence interactions both increase 4-fold. The database can be accessed interactively through a web interface, displaying interactions in an integrated network view. It is also available for computational studies through downloadable files and an API. As an extension in the current version, we offer the option to switch between two levels of detail, namely whether stereoisomers of a given compound are shown as a merged entity or as separate entities. Separate display of stereoisomers is necessary, for example, for carbohydrates and chiral drugs. Combining the isomers increases the coverage, as interaction databases and publications found through text mining will often refer to compounds without specifying the stereoisomer. The database is accessible at http://stitch.embl.de/.

AB - To facilitate the study of interactions between proteins and chemicals, we have created STITCH, an aggregated database of interactions connecting over 300,000 chemicals and 2.6 million proteins from 1133 organisms. Compared to the previous version, the number of chemicals with interactions and the number of high-confidence interactions both increase 4-fold. The database can be accessed interactively through a web interface, displaying interactions in an integrated network view. It is also available for computational studies through downloadable files and an API. As an extension in the current version, we offer the option to switch between two levels of detail, namely whether stereoisomers of a given compound are shown as a merged entity or as separate entities. Separate display of stereoisomers is necessary, for example, for carbohydrates and chiral drugs. Combining the isomers increases the coverage, as interaction databases and publications found through text mining will often refer to compounds without specifying the stereoisomer. The database is accessible at http://stitch.embl.de/.

KW - Biochemical Processes

KW - Databases, Protein

KW - Pharmaceutical Preparations

KW - Proteins

KW - Stereoisomerism

U2 - 10.1093/nar/gkr1011

DO - 10.1093/nar/gkr1011

M3 - Journal article

C2 - 22075997

SN - 0305-1048

VL - 40

SP - D876-80

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - Database issue

ER -