VarSite: Disease variants and protein structure

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. The analyses are primarily image‐based and provide both an overview for each human protein, as well as a report...

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Bibliographic Details
Published in:Protein science 2020-01, Vol.29 (1), p.111-119
Main Authors: Laskowski, Roman A., Stephenson, James D., Sillitoe, Ian, Orengo, Christine A., Thornton, Janet M.
Format: Article
Language:English
Subjects:
3D protein structure
Annotations
CATH
ClinVar
Cloud Computing
Computational Biology
Databases, Genetic
Deoxyribonucleic acid
disease variants
DNA
Domains
Genetic Predisposition to Disease
Genetic Variation
gnomAD
Humans
Internet
Models, Molecular
molecular interactions
natural variants
PDB
Peptide mapping
Pfam
Protein Conformation
Protein structure
Proteins
Proteins - chemistry
Proteins - genetics
Ribonucleic acid
RNA
schematic diagrams
Secondary structure
Servers
Tools for Protein Science
UniProt
User-Computer Interface
VarMap
VarSite
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Description
Summary: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. 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.
ISSN:0961-8368
1469-896X
DOI:10.1002/pro.3746