Dataset Information

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.

SUBMITTER: Das AA

PROVIDER: S-EPMC4357787 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature

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PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions.

Das Arindam Atanu AA Sharma Om Prakash OP Kumar Muthuvel Suresh MS Krishna Ramadas R Mathur Premendu P PP

Genomics, proteomics & bioinformatics 20130726 4

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 ...[more]

PMID: 23896518

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Project description:BACKGROUND: Human protein-protein interaction (PPIs) data are the foundation for understanding molecular signalling networks and the functional roles of biomolecules. Several human PPI databases have become available; however, comparisons of these datasets have suggested limited data coverage and poor data quality. Ongoing collection and integration of human PPIs from different sources, both experimentally and computationally, can enable disease-specific network biology modelling in translational bioinformatics studies. RESULTS: We developed a new web-based resource, the Human Annotated and Predicted Protein Interaction (HAPPI) database, located at http://bio.informatics.iupui.edu/HAPPI/. The HAPPI database was created by extracting and integrating publicly available protein interaction databases, including HPRD, BIND, MINT, STRING, and OPHID, using database integration techniques. We designed a unified entity-relationship data model to resolve semantic level differences of diverse concepts involved in PPI data integration. We applied a unified scoring model to give each PPI a measure of its reliability that can place each PPI at one of the five star rank levels from 1 to 5. We assessed the quality of PPIs contained in the new HAPPI database, using evolutionary conserved co-expression pairs called "MetaGene" pairs to measure the extent of MetaGene pair and PPI pair overlaps. While the overall quality of the HAPPI database across all star ranks is comparable to the overall qualities of HPRD or IntNetDB, the subset of the HAPPI database with star ranks between 3 and 5 has a much higher average quality than all other human PPI databases. As of summer 2008, the database contains 142,956 non-redundant, medium to high-confidence level human protein interaction pairs among 10,592 human proteins. The HAPPI database web application also provides ..." should be "The HAPPI database web application also provides hyperlinked information of genes, pathways, protein domains, protein structure displays, and sequence feature maps for interactive exploration of PPI data in the database. CONCLUSION: HAPPI is by far the most comprehensive public compilation of human protein interaction information. It enables its users to fully explore PPI data with quality measures and annotated information necessary for emerging network biology studies.

Dataset Information

PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions.

Publications

PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions.

Similar Datasets

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