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SNPeffect


NAR Molecular Biology Database Collection entry number 626
De Baets, Greet1,2,3; Van Durme, Joost1,2,3; Reumers, Joke4,5; Maurer-Stroh, Sebastian6; Vanhee, Peter1,3; Dopazo, Joaquin7,8; Schymkowitz, Joost1,2 and Rousseau, Frederic1,2
1VIB Switch Laboratory, 3000 Leuven, 2Department of Molecular Cell Biology, University of Leuven, 3Vrije Universiteit Brussel, 4Vesalius Research Center, VIB, 3000 Leuven, 5Vesalius Research Center, University of Leuven, Belgium, 6Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, 7Department of Bioinformatics, Centro de Investigación Príncipe Felipe (CIPF) and 8Functional Genomics Node (INB) at CIPF, Valencia 46013, Spain

Database Description

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.

Recent Developments

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.

Acknowledgements

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 2012 Database Issue.
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