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
Wed Jan 21 2010:
PolyPhen service is now back online.
Wed Jan 20 2010:
Due to hardware failure on our file server, PolyPhen is currently unavailable. Please be patient and allow us 2-3 days to remedy the situation. We apologize for the inconvenience.
Tue Mar 11 2008:
We now have a beta version of Perl scripts for automated batch query submission and retrieval. Please e-mail us if you wish to try them.
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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
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 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