title: XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data.
abstract: Large-scale chemical cross-linking with mass spectrometry (XL-MS) analyses are quickly becoming a powerful means for high-throughput determination of protein structural information and protein-protein interactions. Recent studies have garnered thousands of cross-linked interactions, yet the field lacks an effective tool to compile experimental data or access the network and structural knowledge for these large scale analyses. We present XLinkDB 2.0 which integrates tools for network analysis, Protein Databank queries, modeling of predicted protein structures and modeling of docked protein structures. The novel, integrated approach of XLinkDB 2.0 enables the holistic analysis of XL-MS protein interaction data without limitation to the cross-linker or analytical system used for the analysis.
  
  
  
  XLinkDB 2.0 can be found here, including documentation and help: http://xlinkdb.gs.washington.edu/
  
  
  
  : jimbruce@uw.edu
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA.
authors.forename: Devin K
authors.initials: DK
authors.lastname: Schweppe
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA.
authors.forename: Chunxiang
authors.initials: C
authors.lastname: Zheng
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA.
authors.forename: Juan D
authors.initials: JD
authors.lastname: Chavez
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA.
authors.forename: Arti T
authors.initials: AT
authors.lastname: Navare
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA.
authors.forename: Xia
authors.initials: X
authors.lastname: Wu
authors.affiliation: University of Washington Proteomics Resource, Seattle, WA 98109, USA.
authors.forename: Jimmy K
authors.initials: JK
authors.lastname: Eng
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA.
authors.forename: James E
authors.initials: JE
authors.lastname: Bruce
mesh_terms: D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D003432:Cross-Linking Reagents; D030562:Databases, Protein; D006801:Humans; D013058:Mass Spectrometry; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins; D012984:Software
chemical_list: D003432:Cross-Linking Reagents; D011506:Proteins