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VarMod: modelling the functional effects of non-synonymous variants.

Pappalardo, M., Wass, Mark N. (2014) VarMod: modelling the functional effects of non-synonymous variants. Nucleic Acids Research, 42 (W1). W331-W336. ISSN 0305-1048. E-ISSN 1362-4962. (doi:10.1093/nar/gku483)

Abstract

Unravelling the genotype–phenotype relationship in humans remains a challenging task in genomics studies. Recent advances in sequencing technologies mean there are now thousands of sequenced human genomes, revealing millions of single nucleotide variants (SNVs). For non-synonymous SNVs present in proteins the difficulties of the problem lie in first identifying those nsSNVs that result in a functional change in the protein among the many non-functional variants and in turn linking this functional change to phenotype. Here we present VarMod (Variant Modeller) a method that utilises both protein sequence and structural features to predict nsSNVs that alter protein function. VarMod develops recent observations that functional nsSNVs are enriched at protein–protein interfaces and protein–ligand binding sites and uses these characteristics to make predictions. In benchmarking on a set of nearly 3000 nsSNVs VarMod performance is comparable to an existing state of the art method. The VarMod web server provides extensive resources to investigate the sequence and structural features associated with the predictions including visualisation of protein models and complexes via an interactive JSmol molecular viewer.

VarMod is available for use at http://www.wasslab.org/varmod.

Item Type: Article
DOI/Identification number: 10.1093/nar/gku483
Subjects: Q Science
Divisions: Faculties > Sciences > School of Biosciences
Depositing User: Mark Wass
Date Deposited: 03 Aug 2014 11:20 UTC
Last Modified: 07 Feb 2020 16:10 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/42078 (The current URI for this page, for reference purposes)
Wass, Mark N.: https://orcid.org/0000-0001-5428-6479
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