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.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.