NDLI: SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein

Content Provider	PubMed Central
Author	Jefferson, Emily R. Walsh, Thomas P. Roberts, Timothy J. Barton, Geoffrey J.
Copyright Year	2006
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: .
Related Links	http://dx.doi.org/10.1093/nar/gkl836
Starting Page	580
File Format	PDF
ISSN	03051048
e-ISSN	13624962
Journal	Nucleic Acids Research
Issue Number	Database issue
Volume Number	35
Language	English
Publisher	Oxford University Press
Publisher Date	2007-01-03
Access Restriction	Open
Rights Holder	Oxford University Press
Subject Keyword	Genetics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics

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SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein–Protein Interactions

TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method

DMAPS: a database of multiple alignments for protein structures

PCRPi-DB: a database of computationally annotated hot spots in protein interfaces

TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method

DMAPS: a database of multiple alignments for protein structures

The PSSH database of alignments between protein sequences and tertiary structures

PCRPi-DB: a database of computationally annotated hot spots in protein interfaces

OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures

SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein–Protein Interactions

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SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein–Protein Interactions

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SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein–Protein Interactions