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Bioinformatics. 2016 Jan 15;32(2):306-8. doi: 10.1093/bioinformatics/btv519. Epub 2015 Sep 26.

XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking.

Author information

1
Department of Genome Sciences, University of Washington, 850 Republican Ave, Seattle, WA 98109, USA.

Abstract

MOTIVATION:

Chemical cross-linking with mass spectrometry (XL-MS) provides structural information for proteins and protein complexes in the form of crosslinked residue proximity and distance constraints between reactive residues. Utilizing spatial information derived from cross-linked residues can therefore assist with structural modeling of proteins. Selection of computationally derived model structures of proteins remains a major challenge in structural biology. The comparison of site interactions resulting from XL-MS with protein structure contact maps can assist the selection of structural models.

AVAILABILITY AND IMPLEMENTATION:

XLmap was implemented in R and is freely available at: http://brucelab.gs.washington.edu/software.php.

CONTACT:

jimbruce@uw.edu

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
26411867
PMCID:
PMC5013974
DOI:
10.1093/bioinformatics/btv519
[Indexed for MEDLINE]
Free PMC Article

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