title: PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions.
abstract: Protein-peptide interactions, where one partner is a globular protein (domain) and the other is a flexible linear peptide, are key components of cellular processes predominantly in signaling and regulatory networks, hence are prime targets for drug design. To derive the details of the protein-peptide interaction mechanism is often a cumbersome task, though it can be made easier with the availability of specific databases and tools. The Peptide Binding Protein Database (PepBind) is a curated and searchable repository of the structures, sequences and experimental observations of 3100 protein-peptide complexes. The web interface contains a computational tool, protein inter-chain interaction (PICI), for computing several types of weak or strong interactions at the protein-peptide interaction interface and visualizing the identified interactions between residues in Jmol viewer. This initial database release focuses on providing protein-peptide interface information along with structure and sequence information for protein-peptide complexes deposited in the Protein Data Bank (PDB). Structures in PepBind are classified based on their cellular activity. More than 40% of the structures in the database are found to be involved in different regulatory pathways and nearly 20% in the immune system. These data indicate the importance of protein-peptide complexes in the regulation of cellular processes.
authors.affiliation: Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry 605014, India.
authors.forename: Arindam Atanu
authors.initials: AA
authors.lastname: Das
authors.forename: Om Prakash
authors.initials: OP
authors.lastname: Sharma
authors.forename: Muthuvel Suresh
authors.initials: MS
authors.lastname: Kumar
authors.forename: Ramadas
authors.initials: R
authors.lastname: Krishna
authors.forename: Premendu P
authors.initials: PP
authors.lastname: Mathur
mesh_terms: D030562:Databases, Protein; D020407:Internet; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D054730:Protein Interaction Domains and Motifs; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012985:Software Design
chemical_list: D010455:Peptides; D011506:Proteins
keywords: PepBind; Peptide-binding proteins database; Protein inter-chain interaction; Protein–peptide complex; Protein–peptide interaction tool; Protein–peptide interface
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