{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Schiffrin B"],"funding":["University of Leeds","Biotechnology and Biological Sciences Research Council"],"pagination":["1851-1857"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC7380677"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["29(8)"],"pubmed_abstract":["Chemical crosslinking-mass spectrometry (XL-MS) is a valuable technique for gaining insights into protein structure and the organization of macromolecular complexes. XL-MS data yield inter-residue restraints that can be compared with high-resolution structural data. Distances greater than the crosslinker spacer-arm can reveal lowly populated \"excited\" states of proteins/protein assemblies, or crosslinks can be used as restraints to generate structural models in the absence of structural data. Despite increasing uptake of XL-MS, there are few tools to enable rapid and facile mapping of XL-MS data onto high-resolution structures or structural models. PyXlinkViewer is a user-friendly plugin for PyMOL v2 that maps intra-protein, inter-protein, and dead-end crosslinks onto protein structures/models and automates the calculation of inter-residue distances for the detected crosslinks. This enables rapid visualization of XL-MS data, assessment of whether a set of detected crosslinks is congruent with structural data, and easy production of high-quality images for publication."],"journal":["Protein science : a publication of the Protein Society"],"pubmed_title":["PyXlinkViewer: A flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system."],"pmcid":["PMC7380677"],"funding_grant_id":["BB/T000635/1","BB/N007603/1","BB/P000037/1"],"pubmed_authors":["Radford SE","Brockwell DJ","Calabrese AN","Schiffrin B"],"additional_accession":[]},"is_claimable":false,"name":"PyXlinkViewer: A flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system.","description":"Chemical crosslinking-mass spectrometry (XL-MS) is a valuable technique for gaining insights into protein structure and the organization of macromolecular complexes. XL-MS data yield inter-residue restraints that can be compared with high-resolution structural data. Distances greater than the crosslinker spacer-arm can reveal lowly populated \"excited\" states of proteins/protein assemblies, or crosslinks can be used as restraints to generate structural models in the absence of structural data. Despite increasing uptake of XL-MS, there are few tools to enable rapid and facile mapping of XL-MS data onto high-resolution structures or structural models. PyXlinkViewer is a user-friendly plugin for PyMOL v2 that maps intra-protein, inter-protein, and dead-end crosslinks onto protein structures/models and automates the calculation of inter-residue distances for the detected crosslinks. This enables rapid visualization of XL-MS data, assessment of whether a set of detected crosslinks is congruent with structural data, and easy production of high-quality images for publication.","dates":{"release":"2020-01-01T00:00:00Z","publication":"2020 Aug","modification":"2024-11-20T16:20:46.464Z","creation":"2020-11-08T09:37:39Z"},"accession":"S-EPMC7380677","cross_references":{"pubmed":["32557917"],"doi":["10.1002/pro.3902"]}}