STITCH 3: zooming in on protein-chemical interactions

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

STITCH 3 : zooming in on protein-chemical interactions. / Kuhn, Michael; Szklarczyk, Damian; Franceschini, Andrea; von Mering, Christian; Jensen, Lars Juhl; Bork, Peer.

In: Nucleic Acids Research, Vol. 40, No. Database issue, 2012, p. D876-80.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Kuhn, M, Szklarczyk, D, Franceschini, A, von Mering, C, Jensen, LJ & Bork, P 2012, 'STITCH 3: zooming in on protein-chemical interactions', Nucleic Acids Research, vol. 40, no. Database issue, pp. D876-80. https://doi.org/10.1093/nar/gkr1011

APA

Kuhn, M., Szklarczyk, D., Franceschini, A., von Mering, C., Jensen, L. J., & Bork, P. (2012). STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Research, 40(Database issue), D876-80. https://doi.org/10.1093/nar/gkr1011

Vancouver

Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P. STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Research. 2012;40(Database issue):D876-80. https://doi.org/10.1093/nar/gkr1011

Author

Kuhn, Michael ; Szklarczyk, Damian ; Franceschini, Andrea ; von Mering, Christian ; Jensen, Lars Juhl ; Bork, Peer. / STITCH 3 : zooming in on protein-chemical interactions. In: Nucleic Acids Research. 2012 ; Vol. 40, No. Database issue. pp. D876-80.

Bibtex

@article{f528c2ecd88141f3aff4c06d90d9e792,
title = "STITCH 3: zooming in on protein-chemical interactions",
abstract = "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/.",
keywords = "Biochemical Processes, Databases, Protein, Pharmaceutical Preparations, Proteins, Stereoisomerism",
author = "Michael Kuhn and Damian Szklarczyk and Andrea Franceschini and {von Mering}, Christian and Jensen, {Lars Juhl} and Peer Bork",
year = "2012",
doi = "10.1093/nar/gkr1011",
language = "English",
volume = "40",
pages = "D876--80",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "Database issue",

}

RIS

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

Y1 - 2012

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

VL - 40

SP - D876-80

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - Database issue

ER -

ID: 40290926