NAR Molecular Biology Database Collection entry number 626

http://snpeffect.vib.be/

J. Reumers¹, J. Schymkowitz¹, L. Serrano², J. Borg³, F. Stricher² and F. Rousseau¹

¹ Switch Laboratory, Flemish Interuniversity Institute for Biotechnology (VIB), Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
² European Molecular Biology Laboratory, Meyerhofstrasse 1, 62119 Heidelberg, Germany
³ Niels Bohr Institute, Blegdamsvey 17, Copenhagen, DK-2100 Denmark.

Contact frederic.rousseau@vub.ac.be

SNPeffect uses computational tools to analyse the effect of coding, non-synonymous SNPs on 3 categories of functional and physico-chemical properties of the affected proteins:
- Protein Structure and Dynamics: protein stability (FOLDX), beta-aggregation (TANGO) and amyloidosis (AmyScan).
- Integrity of Functional Sites: Catalytic (CSA) and binding sites (Hsp70, ELM).
- Cellular Processing: subcellular localisation (PA subcellular), turnover rate (N-terminal rule), post-translational modifcations (O-GlycBase, Phosphobase).
Links to the OMIM, PFAM, PDB and SWISSPROT are provided where available.

Future work will aim at including high quality homology models generated using FoldX to increase the structural information available in SNPeffect. The list of properties analysed is continually being extended and will soon include protein folding and dynamics, metal ion binding, protein-protein interactions, protein-DNA interactions. Subsequently, we will also create a mouse SNPeffect database. The database will be regularly updated as new SNP data and information on phenotypic effects will become available.

We are grateful to Dr. Manuela Lopez de la Paz for pre-publication use of AmyScan. We would also like to thank Luc Van Wiemeersch and Els Herregods for help with setting up the computing facilities.

Go to the abstract in the NAR 2008 Database Issue.

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