Bork Group
Sunyaev Lab
PolyPhen: prediction of functional effect
of human nsSNPs
PolyPhen (=Polymorphism Phenotyping) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations
Tue Jul 20 18:46:59 EDT 2010:
Dear PolyPhen users! Please be aware that this version of the server is no longer maintained nor updated and will be soon discontinued. You are welcome to switch to PolyPhen-2 instead.
Sat May 1 21:30:00 EDT 2010:
Batch query interface to PolyPhen-2 server now accepts genomic SNP coordinates as input, as well as dbSNP reference SNP numbers (rsIDs). Precomputed dbSNP build 131 PolyPhen-2 annotations for human missense SNPs are accessible via dbSNP query quick search page and can be downloaded here.
Wed Mar 31 07:29:00 EDT 2010:
New version of the PolyPhen web server has been released. PolyPhen-2 includes numerous improvements, as well as a simple and efficient batch query web interface. Also available as a standalone software for Linux / Mac OS X. We would appreciate your feedback.
Links Query data
Help
PolyPhen description

SNP data collection
Precomputed data for human nsSNPs from dbSNP database

References
Papers on the method

SNP2Prot
A tool to map human DNA variation onto proteins. Please use it if you start with DNA sequences and are not sure whether your SNP is non-synonymous

dbSNP Database
Single Nucleotide Polymorphism Database at NCBI

Examples
Examples of PolyPhen output

Database statistics
Statistics on databases used by PolyPhen

Feedback
E-mail us

Protein identifier (accession or name) from the UniProt database
 OR

Amino acid sequence in FASTA format

Position   Substitution  AA1   AA2 

Description 

          
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Query options
Structural database   PQS PDB
Sort hits by   Identity E-value
Map to mismatch   No Yes
Calculate structural parameters   For first hit only For all hits
Calculate contacts   For first hit only For all hits
Minimal alignment length    
Minimal identity in alignment    
Maximal gap length in alignment    
Threshold for contacts     Å