PPInS Edit

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Basic information
Short name PPInS
Full name
Description a repository of protein-protein interaction sitesbase.
URL http://www.cup.edu.in:99/ppins/home.php
Year founded
Last update & version
Availability Free to academic users only
Contact information
University/Institution hosted Central University of Punjab
Address
City
Province/State
Country/Region India
Contact name Mahesh Kulharia
Contact email kulharia@gmail.com
Data information
Data object
  • NA
Data type
  • Protein
Database category
  • Interaction
Major organism
  • NA
Keyword
  • protein-protein
Publications
  • PPInS: a repository of protein-protein interaction sitesbase. [PMID: 30127348]
    Vicky Kumar, Suchismita Mahato, Anjana Munshi, Mahesh Kulharia

    Protein-Protein Interaction Sitesbase (PPInS), a high-performance database of protein-protein interacting interfaces, is presented. The atomic level information of the molecular interaction happening amongst various protein chains in protein-protein complexes (as reported in the Protein Data Bank [PDB]) together with their evolutionary information in Structural Classification of Proteins (SCOPe release 2.06), is made available in PPInS. Total 32468 PDB files representing X-ray crystallized multimeric protein-protein complexes with structural resolution better than 2.5 Å had been shortlisted to demarcate the protein-protein interaction interfaces (PPIIs). A total of 111857 PPIIs with ~32.24 million atomic contact pairs (ACPs) were generated and made available on a web server for on-site analysis and downloading purpose. All these PPIIs and protein-protein interacting patches (PPIPs) involved in them, were also analyzed in terms of a number of residues contributing in patch formation, their hydrophobic nature, amount of surface area they contributed in binding, and their homo and heterodimeric nature, to describe the diversity of information covered in PPInS. It was observed that 42.37% of total PPIPs were made up of 6-20 interacting residues, 53.08% PPIPs had interface area ≤1000 Å in PPII formation, 82.64% PPIPs were reported with hydrophobicity score of ≤10, and 73.26% PPIPs were homologous to each other with the sequence similarity score ranging from 75-100%. A subset "Non-Redundant Database (NRDB)" of the PPInS containing 2265 PPIIs, with over 1.8 million ACPs corresponding to the 1931 protein-protein complexes (PDBs), was also designed by removing structural redundancies at the level of SCOP superfamily (SCOP release 1.75). The web interface of the PPInS ( http://www.cup.edu.in:99/ppins/home.php ) offers an easy-to-navigate, intuitive and user-friendly environment, and can be accessed by providing PDB ID, SCOP superfamily ID, and protein sequence.

    Sci Rep 2018:8(1)

    0 Citations (from Europe PMC, 2019-01-19)

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  • Created on: 2019-01-15
    • ***d@***c.cn [2019-01-15]
    • ***d@***c.cn [2019-01-15]
    • ***d@***c.cn [2019-01-15]

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