title: XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking.
abstract: BACKGROUND
  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.
  
  
  METHODS
  XLmap was implemented in R and is freely available at: http://brucelab.gs.washington.edu/software.php.
  
  
  BACKGROUND
  jimbruce@uw.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Genome Sciences, University of Washington, 850 Republican Ave, Seattle, WA 98109, USA.
authors.forename: Devin K
authors.initials: DK
authors.lastname: Schweppe
authors.affiliation: Department of Genome Sciences, University of Washington, 850 Republican Ave, Seattle, WA 98109, USA.
authors.forename: Juan D
authors.initials: JD
authors.lastname: Chavez
authors.affiliation: Department of Genome Sciences, University of Washington, 850 Republican Ave, Seattle, WA 98109, USA.
authors.forename: James E
authors.initials: JE
authors.lastname: Bruce
mesh_terms: D003198:Computer Simulation; D003432:Cross-Linking Reagents / Q000737:chemistry*; D030562:Databases, Protein; D006801:Humans; D007091:Image Processing, Computer-Assisted; D013058:Mass Spectrometry / Q000379:methods; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D003432:Cross-Linking Reagents; D011506:Proteins