XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking
Devin K Schweppe1, Juan D Chavez1, James E Bruce1
1Department of Genome Sciences, University of Washington, 850 Republican Ave, Seattle, WA 98109, USA.
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.
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