PolyDoms: Mapping of Human Coding SNPs onto Protein Domains

SNPs
Publicly available SNP database. Currently has about 10 million human SNPs throughout the genome. PolyDoms uses dbSNP for SNP information.

Annotations
Database for gene annotations
Links genes and proteins to pathologies, phenotypes, physiology, and interaction by linking through pubmed abstracts.
The Proteome Browser provides a wealth of protein information presented in the form of graphical images and links to external internet sites.

Allelic Variants
Database of hereditary diseases linked to genes. OMIM contains records linking specific allelic variants of genes to diseases. This database is expert curated and hence has high-quality data. PolyDoms uses this database for finding if the polymorphism is also a known mutation.
An EBI database linking protein's sequence variants to diseases. This database is manually curated.

Mammalian Phenotype
Jackson lab's mouse informatics data.
The Genetic Association Database is an archive of human genetic association studies of complex diseases and disorders. The goal of this database is to allow the user to rapidly identify medically relevant polymorphism from the large volume of polymorphism and mutational data, in the context of standardized nomenclature.

Protein Interactions
BIND is a database designed to store full descriptions of interactions, molecular complexes and pathways. PolyDoms uses this database for obtaining protein-protein interactions.
HPRD is an expert curated database containing interaction networks, disease associations, and post-translation modifications for each protein in the human proteome. PolyDoms primarily uses this database for protein-protein interactions.

Pathways
KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks
BioCyc is a collection of 205 Pathway/Genome Databases describing the genome and the metabolic pathways. PolyDoms uses the HumanCyc database which is a collection of human metabolic pathway s and the genes associated with each one of them.
BioCarta pathways is a database of pathways and the corresponding genes associated with each one of them.
Reactome is a curated resource of core pathways and reactions in human biology. The information in this database is cross-referenced with PubMed, GO, and the sequence databases at NCBI, Ensembl and UniProt. PolyDoms uses this database for obtaining the pathways a gene is associated with.

Protein Structure
The PDB is the single worldwide repository for the processing and distribution of 3-D structure data of large molecules of proteins and nucleic acids. PolyDoms uses PDB for obtaining 3D-structure information of proteins. The coding-SNPs are then mapped to the 3D-Structure.

Prediction of cSNP effect
SIFT is a program that predicts whether an amino acid substitution affects protein function so that users can prioritize substitutions for further study.
PolyPhen 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
LS-SNP is an annotated database of SNPs. Currently only coding non-synonomous SNPs found in human genes are included.

Literature
PubMed is a service of the U.S. National Library of Medicine that includes over 16 million citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. PolyDoms uses pubmed for extracting literature evidence implicating coding SNPs of specific genes with diseases.

Other SNP analysis tools
The goal of MutDB is to annotate human variation data with protein structural information and other functionally relevant information, if available. The mutations are organized by gene.