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Example 1: 1CP3

Number of complexes: 5314
Number of peptides: 5422
Number of distinct domains: 1695
(Based on structural similarity)
Number of distinct peptides: 3442
(Based on sequence similarity)

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Peptide Binding Protein Database (PepBind) is a derived database of available structures of protein-peptide complexes from Protein Data Bank (PDB). These proteins are further classified as per the length of the peptide, such as dipeptide binding proteins, tripeptide binding proteins, etc. Peptides can be defined as follows:

According to MeSH (National Library of Medicine - Medical Subject Headings) description of Peptides:

"Members of the class of compounds composed of amino acids joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. Oligopeptides are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. Proteins are linear polypeptides that are normally synthesized on ribosomes."

PepBind database contains 5314 protein structures and is updating monthly. It contains protein information, Peptide Binding information, Sequence information, Experimental data, Ramachandran Plot, Primary Citation about the protein structure, etc. It also has many interactive search tools which can search the database as per the query of the user. The search tool contains seven different types of search options which simplifies the searching of the database. Links are given for several terms on every page which will search that specific term in the database and give relevant results. Many external links are also provided to other related databases.

This database is created and maintained on LAMP server.


Please cite:

Das AA, Sharma OP, Kumar MS, Krishna R, Mathur PP. PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions. Genomics Proteomics Bioinformatics 2013; 11: 241-6.


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Peptide Binding Protein Database is developed by Center for Bioinformatics, Pondicherry University (India) with the support and funding from Department of Information Technology [grant number DIT/R&D/Bio/15 (9)2007], Government of India.

Researchers can submit data here

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