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VarSite: disease variants and protein structure

Laskowski, RA; Stephenson, JD; Sillitoe, I; Orengo, CA; Thornton, JM; (2020) VarSite: disease variants and protein structure. Protein Science , 29 (1) pp. 111-119. 10.1002/pro.3746. Green open access

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Abstract

VarSite is a web server mapping known disease-associated variants from UniProt and ClinVar, together with natural variants from gnomAD, onto protein 3D structures in the Protein Data Bank (PDB). The analyses are primarily image-based and provide both an overview for each human protein, as well as a report for any specific variant of interest. The information can be useful in assessing whether a given variant might be pathogenic or benign. The structural annotations for each position in the protein include protein secondary structure, interactions with ligand, metal, DNA/RNA, or other protein, and various measures of a given variant's possible impact on the protein's function. The 3D locations of the disease-associated variants can be viewed interactively via the 3dmol.js JavaScript viewer, as well as in RasMol and PyMOL. Users can search for specific variants, or sets of variants, by providing the DNA coordinates of the base change(s) of interest. Additionally, various agglomerative analyses are given, such as the mapping of disease and natural variants onto specific Pfam or CATH domains. The server is freely accessible to all at: https://www.ebi.ac.uk/thornton-srv/databases/VarSite. This article is protected by copyright. All rights reserved.

Type: Article
Title: VarSite: disease variants and protein structure
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1002/pro.3746
Publisher version: https://doi.org/10.1002/pro.3746
Language: English
Additional information: © 2019 The Authors. Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society. This is an open access article under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/).
Keywords: 3D protein structure, CATH, ClinVar, PDB, Pfam, UniProt, VarMap, VarSite, disease variants, gnomAD, molecular interactions, natural variants, schematic diagrams
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology
URI: https://discovery.ucl.ac.uk/id/eprint/10084094
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