MOTIVATION: 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. AVAILABILITY AND IMPLEMENTATION: XLinkDB 2.0 can be found here, including documentation and help: http://xlinkdb.gs.washington.edu/ CONTACT: : jimbruce@uw.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: 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. AVAILABILITY AND IMPLEMENTATION: XLinkDB 2.0 can be found here, including documentation and help: http://xlinkdb.gs.washington.edu/ CONTACT: : jimbruce@uw.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Juan D Chavez; Chad R Weisbrod; Chunxiang Zheng; Jimmy K Eng; James E Bruce Journal: Mol Cell Proteomics Date: 2013-01-25 Impact factor: 5.911
Authors: Chad R Weisbrod; Juan D Chavez; Jimmy K Eng; Li Yang; Chunxiang Zheng; James E Bruce Journal: J Proteome Res Date: 2013-02-28 Impact factor: 4.466
Authors: Arti T Navare; Juan D Chavez; Chunxiang Zheng; Chad R Weisbrod; Jimmy K Eng; Richard Siehnel; Pradeep K Singh; Colin Manoil; James E Bruce Journal: Structure Date: 2015-03-19 Impact factor: 5.006
Authors: Devin K Schweppe; Christopher Harding; Juan D Chavez; Xia Wu; Elizabeth Ramage; Pradeep K Singh; Colin Manoil; James E Bruce Journal: Chem Biol Date: 2015-11-05
Authors: Daniel Russel; Keren Lasker; Ben Webb; Javier Velázquez-Muriel; Elina Tjioe; Dina Schneidman-Duhovny; Bret Peterson; Andrej Sali Journal: PLoS Biol Date: 2012-01-17 Impact factor: 8.029
Authors: Xuefei Zhong; Arti T Navare; Juan D Chavez; Jimmy K Eng; Devin K Schweppe; James E Bruce Journal: J Proteome Res Date: 2016-11-30 Impact factor: 4.466
Authors: Juan D Chavez; Jared P Mohr; Martin Mathay; Xuefei Zhong; Andrew Keller; James E Bruce Journal: Nat Protoc Date: 2019-07-03 Impact factor: 13.491