XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data

• DOI: 10.1093/bioinformatics/btw232
• Publication Date: 2016-04-30T01:35:22Z
• Authors: Devin K. Schweppe; Chunxiang Zheng; Juan D. Chavez; Arti T. Navare; Xia Wu; Jimmy K. Eng; James E. Bruce
• Keywords: Models, Molecular; 0301 basic medicine; 03 medical and health sciences; Cross-Linking Reagents; Protein Conformation; Computational Biology; Humans; Proteins; Computer Simulation; Databases, Protein; Mass Spectrometry; Software

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 cross-linked interactions, yet the field lacks an effective tool to compile experimental data or access network knowledge these large scale analyses. We present XLinkDB 2.0 which integrates tools analysis, Protein Databank queries, modeling predicted structures docked structures. The novel, integrated approach enables holistic analysis XL-MS interaction without limitation cross-linker analytical system used analysis.XLinkDB can be found here, including documentation help: http://xlinkdb.gs.washington.edu/: [e-mail] available at Bioinformatics online.