title: Xwalk: computing and visualizing distances in cross-linking experiments.
abstract: BACKGROUND
  Chemical cross-linking of proteins or protein complexes and the mass spectrometry-based localization of the cross-linked amino acids in peptide sequences is a powerful method for generating distance restraints on the substrate's topology.
  
  
  RESULTS
  Here, we introduce the algorithm Xwalk for predicting and validating these cross-links on existing protein structures. Xwalk calculates and displays non-linear distances between chemically cross-linked amino acids on protein surfaces, while mimicking the flexibility and non-linearity of cross-linker molecules. It returns a 'solvent accessible surface distance', which corresponds to the length of the shortest path between two amino acids, where the path leads through solvent occupied space without penetrating the protein surface.
  
  
  BACKGROUND
  Xwalk is freely available as a web server or stand-alone JAVA application at http://www.xwalk.org.
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH Zurich), CH-8093 Zurich, Switzerland. abdullah@imsb.biol.ethz.ch
authors.forename: Abdullah
authors.initials: A
authors.lastname: Kahraman
authors.forename: Lars
authors.initials: L
authors.lastname: Malmström
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods*; D020407:Internet; D013058:Mass Spectrometry; D011381:Programming Languages; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D000596:Amino Acids; D011506:Proteins