October 2015

SAAPpred is now available via SAAPdap

Single Amino Acid Polymorphisms (SAAPs)

The Resources


Analysis of the effects of a mutation (SAAPdap)

Using a PDB file and the nature of a mutation, the local structural effects of the mutation are analyzed as follows:

The analysis methods are described in the following papers:

Prediction of the pathogenicity of mutations (SAAPpred)

The results of the SAAPdap structural analysis are fed into a Random Forest machine learning algorithm in order to predict whether a mutation is damaging.

Links and related resources

We have assembled a reasonably comprehensive list of methods for predicting the effects of mutations.

Other resources:


SAAPdb is no longer maintained.

The SAAP database was a Wellcome Trust funded project to integrate information on Single Amino Acid Polymorphisms (i.e. structurally expressed SNPs and mutations) with analysis of the likely structural effects of these amino acid mutations.

The project gathered data on SNPs from dbSNP and HGVBASE and mapped the data onto the translated regions of the gene to determine whether the mutation was in a part of the gene translated to protein (in exon) and, if so, whether it causes a missense mutation in the protein. Once this had been determined, the location of the mutation within the protein sequence could be established.

Disease-related mutation data from OMIM were also included in the database.

'Locus Specific Mutation Databases' (LSMDs) provided an additional source of protein mutation data. However, because the formats of these are so diverse, only a limited number were included.

Once the mapping of a mutation to a protein sequence has been achieved, if a structure exists in the Protein Databank for the protein, the mutant is mapped onto the protein and a structural analysis is performed.

Mapping of mutations to sequence and structure

The mapping process is described in the following publications:

Software architecture