PIBASE Edit

Citations: 101

z-index: 7.21

Basic information
Short name PIBASE
Full name Relational Database of Structurally Defined Protein interfaces
Description a collection of all protein structural interfaces extracted from the Protein Data Bank and PQS structure databases
URL http://salilab.org/pibase
Year founded 2015
Last update & version
Accessibility Accessible
Contact information

The contact information is provided to facilitate update of database information, and it is curated based on the contact details in the database or the related publications. To ensure effective contact with database constructors, we give priority to the contact details in the database.

University/Institution University of California San Francisco
Address
City
Province/State
Country/Region United States
Contact name (PI/Team) Andrej Sali
Contact email (PI/Helpdesk) sali@salilab.org
Data information
Data object
Data type
Database category
Major organism
Keyword
Publications
  • PIBASE: a comprehensive database of structurally defined protein interfaces. [PMID: 15657096]
    Fred P Davis, Andrej Sali,

    MOTIVATION: In recent years, the Protein Data Bank (PDB) has experienced rapid growth. To maximize the utility of the high resolution protein-protein interaction data stored in the PDB, we have developed PIBASE, a comprehensive relational database of structurally defined interfaces between pairs of protein domains. It is composed of binary interfaces extracted from structures in the PDB and the Probable Quaternary Structure server using domain assignments from the Structural Classification of Proteins and CATH fold classification systems.
    RESULTS: PIBASE currently contains 158,915 interacting domain pairs between 105,061 domains from 2125 SCOP families. A diverse set of geometric, physiochemical and topologic properties are calculated for each complex, its domains, interfaces and binding sites. A subset of the interface properties are used to remove interface redundancy within PDB entries, resulting in 20,912 distinct domain-domain interfaces. The complexes are grouped into 989 topological classes based on their patterns of domain-domain contacts. The binary interfaces and their corresponding binding sites are categorized into 18,755 and 30,975 topological classes, respectively, based on the topology of secondary structure elements. The utility of the database is illustrated by outlining several current applications.
    AVAILABILITY: The database is accessible via the world wide web at http://salilab.org/pibase
    SUPPLEMENTARY INFORMATION: http://salilab.org/pibase/suppinfo.html.

    Bioinformatics 2005:21(9)

    101 Citations (from Europe PMC, 2019-06-22)

Rank

  • Ranking in all databases: No. 920
  • Ranking in category/categories:
    • Structure: No. 102
    • Interaction: No. 147
The box plots depict Z-index distribution for all databases in Database Commons and for specific database category/categories. The red line indicates log2(Z-index) of PIBASE.

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Record metadata

  • Created on: 2018-02-14
    • ***d@***c.cn [2019-06-11]
    • ***d@***c.cn [2018-02-13]

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