January 2008

The SAAP Database is now fully implemented and ready for use with the latest data.

The Single Amino Acid Polymorphism Database: SAAPdb

Access the Database

Access the web interface here.

Introduction

The SAAP database is 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 gathers data on SNPs from dbSNP and HGVBASE and maps the data onto the translated regions of the gene to determine whether the mutation is 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 has been determined, the location of the mutation within the protein sequence can be established.

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

Locus Specific Mutation Databases (LSMDs) provide an additional source of protein mutation data. However, because the formats of these are so diverse, only a limited number are currently included. It is hoped that a future project will address this problem.

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.


Implementation

Mapping of mutations to sequence and structure

The mapping process is described in the following publications:

Analysis of the effects of a mutation

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:

Software architecture

Links and related resources


Access the web interface here.