title: SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants.
abstract: Single nucleotide variants (SNVs) are, together with copy number variation, the primary source of variation in the human genome and are associated with phenotypic variation such as altered response to drug treatment and susceptibility to disease. Linking structural effects of non-synonymous SNVs to functional outcomes is a major issue in structural bioinformatics. The SNPeffect database (http://snpeffect.switchlab.org) uses sequence- and structure-based bioinformatics tools to predict the effect of protein-coding SNVs on the structural phenotype of proteins. It integrates aggregation prediction (TANGO), amyloid prediction (WALTZ), chaperone-binding prediction (LIMBO) and protein stability analysis (FoldX) for structural phenotyping. Additionally, SNPeffect holds information on affected catalytic sites and a number of post-translational modifications. The database contains all known human protein variants from UniProt, but users can now also submit custom protein variants for a SNPeffect analysis, including automated structure modeling. The new meta-analysis application allows plotting correlations between phenotypic features for a user-selected set of variants.
authors.affiliation: VIB Switch Laboratory, 3000 Leuven, Belgium.
authors.forename: Greet
authors.initials: G
authors.lastname: De Baets
authors.forename: Joost
authors.initials: J
authors.lastname: Van Durme
authors.forename: Joke
authors.initials: J
authors.lastname: Reumers
authors.forename: Sebastian
authors.initials: S
authors.lastname: Maurer-Stroh
authors.forename: Peter
authors.initials: P
authors.lastname: Vanhee
authors.forename: Joaquin
authors.initials: J
authors.lastname: Dopazo
authors.forename: Joost
authors.initials: J
authors.lastname: Schymkowitz
authors.forename: Frederic
authors.initials: F
authors.lastname: Rousseau
mesh_terms: D030562:Databases, Protein; D006801:Humans; D020407:Internet; D015201:Meta-Analysis as Topic; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D011487:Protein Conformation; D011506:Proteins / Q000235:genetics*
chemical_list: D011506:Proteins
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