What is SNAPPI-DB?
SNAPPI-DB is an object-oriented database of domain-domain interactions observed in structural data.
The generation of SNAPPI-DB
The structural data is obtained from the MSD data warehouse as the MSD provides consistent data with links to many types of data about proteins and
nucleic acids. In order to increase performance and allow complex
analysis with a high degree of abstraction, the relevant (and most frequently
queried) data from the MSD is
migrated to an object-oriented database developed using the Java
Data Objects Technology (JDO). Domain-domain interactions are then determined based on atom-atom distances and the interactions stored. The domain-domain interactions are then classified by family pair and interaction interface and multiple alignments are then generated for each group.
What does SNAPPI-DB Contain?
For an in-depth look at the what is contained within SNAPPI-DB and the structure of the relationships between each component please look at the API documentation
- Structural information on all (up to a specific date) structures held in the PDB down to the level of atom co-ordinates.
- Protein Quaternary
Structures (PQS) generated structures
- SCOP, CATH and Pfam domains
- Domains classified to different levels of similarity based on the SCOP and CATH hierarchical classification system and family level for Pfam.
- Interpro regions/domains
- GO terms
- Swissprot identifiers and numbering
- Domain-domain interactions determined for SCOP, CATH and Pfam domains down to the level of which atoms are interacting.
- Domain-domain interactions classified to different levels of similarity based on the SCOP and CATH hierarchical classification system and family level for Pfam.
- Domain-domain interactions classified by their interfacing interfaces (orientation by which they are interacting)
- Multiple structural alignments of domain interactions from each family/superfamily pair for each unique orientation for SCOP, CATH and Pfam domain definitions
- MSD unique numbering to link back to the MSD
What is SNAPPI-DB useful for?
SNAPPI-DB is a useful resource for any analysis of structures but has been opitmised for analysis on domain-domain interactions and domain-ligand interactions. The database has already been employed for 3
studies on the properties of domain-domain interactions and is
currently being employed to train a protein-protein interaction
predictor and a functional residue predictor. SNAPPI-DB has several
features which are not available in other databases including links
to the MSD, speed, being object oriented, storage of multiple domain
definitions and storage of Protein Quaternary
To download the SNAPPI-DB click here.