title: xVis: a web server for the schematic visualization and interpretation of crosslink-derived spatial restraints.
abstract: The identification of crosslinks by mass spectrometry has recently been established as an integral part of the hybrid structural analysis of protein complexes and networks. The crosslinking analysis determines distance restraints between two covalently linked amino acids which are typically summarized in a table format that precludes the immediate and comprehensive interpretation of the topological data. xVis displays crosslinks in clear schematic representations in form of a circular, bar or network diagram. The interactive graphs indicate the linkage sites and identification scores, depict the spatial proximity of structurally and functionally annotated protein regions and the evolutionary conservation of amino acids and facilitate clustering of proteins into subcomplexes according to the crosslink density. Furthermore, xVis offers two options for the qualitative assessment of the crosslink identifications by filtering crosslinks according to identification scores or false discovery rates and by displaying the corresponding fragment ion spectrum of each crosslink for the manual validation of the mass spectrometric data. Our web server provides an easy-to-use tool for the fast topological and functional interpretation of distance information on protein complex architectures and for the evaluation of crosslink fragment ion spectra. xVis is available under a Creative Commons Attribution-ShareAlike 4.0 International license at http://xvis.genzentrum.lmu.de/.
authors.affiliation: Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany.
authors.forename: Maximilian
authors.initials: M
authors.lastname: Grimm
authors.affiliation: Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany.
authors.forename: Tomasz
authors.initials: T
authors.lastname: Zimniak
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland.
authors.forename: Abdullah
authors.initials: A
authors.lastname: Kahraman
authors.affiliation: Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany herzog@genzentrum.lmu.de.
authors.forename: Franz
authors.initials: F
authors.lastname: Herzog
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D042002:Chromatin Assembly and Disassembly; D003196:Computer Graphics; D003432:Cross-Linking Reagents; D006657:Histones / Q000737:chemistry / Q000378:metabolism; D020407:Internet; D013058:Mass Spectrometry; D046912:Multiprotein Complexes / Q000737:chemistry*; D009707:Nucleosomes / Q000737:chemistry / Q000378:metabolism; D012984:Software
chemical_list: D000596:Amino Acids; D003432:Cross-Linking Reagents; D006657:Histones; D046912:Multiprotein Complexes; D009707:Nucleosomes