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J Proteome Res. 2013 Apr 5;12(4):1989-95. doi: 10.1021/pr301162j. Epub 2013 Mar 5.

XLink-DB: database and software tools for storing and visualizing protein interaction topology data.

Author information

1
Department of Chemistry, University of Washington , Seattle, Washington, United States.

Abstract

As large-scale cross-linking data becomes available, new software tools for data processing and visualization are required to replace manual data analysis. XLink-DB serves as a data storage site and visualization tool for cross-linking results. XLink-DB accepts data generated with any cross-linker and stores them in a relational database. Cross-linked sites are automatically mapped onto PDB structures if available, and results are compared to existing protein interaction databases. A protein interaction network is also automatically generated for the entire data set. The XLink-DB server, including examples, and a help page are available for noncommercial use at http://brucelab.gs.washington.edu/crosslinkdbv1/ . The source code can be viewed and downloaded at https://sourceforge.net/projects/crosslinkdb/?source=directory .

PMID:
23413830
PMCID:
PMC3744611
DOI:
10.1021/pr301162j
[Indexed for MEDLINE]
Free PMC Article

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