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. 2012 Apr 3:2012:bas018.
doi: 10.1093/database/bas018. Print 2012.

MSV3d: database of human MisSense Variants mapped to 3D protein structure

Tien-Dao Luu  1 , Alin-Mihai Rusu, Vincent Walter, Raymond Ripp, Luc Moulinier, Jean Muller, Thierry Toursel, Julie D Thompson, Olivier Poch, Hoan Nguyen
Affiliations

MSV3d: database of human MisSense Variants mapped to 3D protein structure

Tien-Dao Luu et al. Database (Oxford). .

Abstract

The elucidation of the complex relationships linking genotypic and phenotypic variations to protein structure is a major challenge in the post-genomic era. We present MSV3d (Database of human MisSense Variants mapped to 3D protein structure), a new database that contains detailed annotation of missense variants of all human proteins (20 199 proteins). The multi-level characterization includes details of the physico-chemical changes induced by amino acid modification, as well as information related to the conservation of the mutated residue and its position relative to functional features in the available or predicted 3D model. Major releases of the database are automatically generated and updated regularly in line with the dbSNP (database of Single Nucleotide Polymorphism) and SwissVar releases, by exploiting the extensive Décrypthon computational grid resources. The database (http://decrypthon.igbmc.fr/msv3d) is easily accessible through a simple web interface coupled to a powerful query engine and a standard web service. The content is completely or partially downloadable in XML or flat file formats. Database URL: http://decrypthon.igbmc.fr/msv3d.

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Figures

Figure 1
Figure 1
General architecture of SM2PH central. SM2PH Central allows the generation of SM2PH instances (focusing on specific sets of target genes) which can access variant information through the new MSV3d, devoted to human variant data and information.
Figure 2
Figure 2
Histogram showing distributions of missense variants by SCOP fold. Each bar contains two parts: the red part represents deleterious substitutions and the green part represents tolerated substitutions.
Figure 3
Figure 3
MSV3d web interface contains numerous functionalities including: (a) field search, (b) free text search, (c) detailed information, (d) 3D structure visualization using Jmol, (e) spatial neighbouring residue visualization, (f) missense annotation service and (g) download service.
Figure 4
Figure 4
Schema of software pipeline.
See this image and copyright information in PMC

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