SNAPPI-DB


17202171	SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. [PMID: 17202171] Jefferson ER, Walsh TP, Roberts TJ, Barton GJ. Abstract SNAPPI-DB, a high performance database of Structures, iNterfaces and Alignments of Protein-Protein Interactions, and its associated Java Application Programming Interface (API) is described. SNAPPI-DB contains structural data, down to the level of atom co-ordinates, for each structure in the Protein Data Bank (PDB) together with associated data including SCOP, CATH, Pfam, SWISSPROT, InterPro, GO terms, Protein Quaternary Structures (PQS) and secondary structure information. Domain-domain interactions are stored for multiple domain definitions and are classified by their Superfamily/Family pair and interaction interface. Each set of classified domain-domain interactions has an associated multiple structure alignment for each partner. The API facilitates data access via PDB entries, domains and domain-domain interactions. Rapid development, fast database access and the ability to perform advanced queries without the requirement for complex SQL statements are provided via an object oriented database and the Java Data Objects (JDO) API. SNAPPI-DB contains many features which are not available in other databases of structural protein-protein interactions. It has been applied in three studies on the properties of protein-protein interactions and is currently being employed to train a protein-protein interaction predictor and a functional residue predictor. The database, API and manual are available for download at: http://www.compbio.dundee.ac.uk/SNAPPI/downloads.jsp. Nucleic Acids Res. 2007:35(Database issue) \| 41 Citations (from Europe PMC, 2025-03-29)

SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. [PMID: 17202171]

Jefferson ER, Walsh TP, Roberts TJ, Barton GJ.

Abstract

SNAPPI-DB, a high performance database of Structures, iNterfaces and Alignments of Protein-Protein Interactions, and its associated Java Application Programming Interface (API) is described. SNAPPI-DB contains structural data, down to the level of atom co-ordinates, for each structure in the Protein Data Bank (PDB) together with associated data including SCOP, CATH, Pfam, SWISSPROT, InterPro, GO terms, Protein Quaternary Structures (PQS) and secondary structure information. Domain-domain interactions are stored for multiple domain definitions and are classified by their Superfamily/Family pair and interaction interface. Each set of classified domain-domain interactions has an associated multiple structure alignment for each partner. The API facilitates data access via PDB entries, domains and domain-domain interactions. Rapid development, fast database access and the ability to perform advanced queries without the requirement for complex SQL statements are provided via an object oriented database and the Java Data Objects (JDO) API. SNAPPI-DB contains many features which are not available in other databases of structural protein-protein interactions. It has been applied in three studies on the properties of protein-protein interactions and is currently being employed to train a protein-protein interaction predictor and a functional residue predictor. The database, API and manual are available for download at: http://www.compbio.dundee.ac.uk/SNAPPI/downloads.jsp.

Nucleic Acids Res. 2007:35(Database issue) | 41 Citations (from Europe PMC, 2025-03-29)

URL:	http://www.compbio.dundee.ac.uk/SNAPPI/downloads.jsp
Full name:	SNAPPI-DB
Description:	SNAPPI-DB is a high performance database of Structures, iNterfaces and Alignments of Protein–Protein Interactions, and its associated Java Application Programming Interface (API). SNAPPI-DB covers all species that had protein 3D structures determined at the time of its creation. Note SNAPPI-DB is no longer updated.
Year founded:	2007
Last update:	2007-01-01
Version:	v1.0
Accessibility:	Accessible
Country/Region:	United Kingdom

Data type:	Protein
Data object:	Animal Archaea Bacteria Fungi Plant Virus
Database category:	Interaction Structure
Major species:	Homo sapiens
Keywords:	Protein Interaction

University/Institution:	University of Dundee
Address:	Dow Street, Dundee, DD1 5EH, Scotland, UK
City:	Dundee
Province/State:	Scotland
Country/Region:	United Kingdom
Contact name (PI/Team):	Geoffrey J. Barton
Contact email (PI/Helpdesk):	gjbarton@dundee.ac.uk

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