PepBind： A Comprehensive Database and Computational Tool for Analysis of Protein-peptide Interactions

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–peptid...

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Vydáno v:	Genomics, proteomics & bioinformatics Ročník 11; číslo 4; s. 241 - 246
Hlavní autoři:	Das, Arindam Atanu, Sharma, Om Prakash, Kumar, Muthuvel Suresh, Krishna, Ramadas, Mathur, Premendu P.
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	China Elsevier Ltd 01.08.2013 Centre of Excellence in Bioinformatics,School of Life Sciences,Pondicherry University,Pondicherry 605014,India%Centre of Excellence in Bioinformatics,School of Life Sciences,Pondicherry University,Pondicherry 605014,India School of Biotechnology,KIIT University,Bhubaneshwar 751024,India Elsevier
Témata:	binding proteins chemistry Databases, Protein drugs immune system Internet metabolism methods Models, Molecular Original Research PepBind Peptide-binding proteins database Peptides Peptides - chemistry Peptides - metabolism Protein inter-chain interaction Protein Interaction Domains and Motifs Protein Interaction Mapping Protein Interaction Mapping - methods protein-protein interactions Proteins Proteins - chemistry Proteins - metabolism Protein–peptide complex Protein–peptide interaction tool Protein–peptide interface Software Design 交互界面序列信息弱相互作用数据库细胞活性蛋白肽蛋白质计算工具 Protein inter-chain interaction Protein–peptide complex Protein–peptide interaction tool PepBind Protein–peptide interface Peptide-binding proteins database Protein-peptide complex Protein-peptide interaction tool Protein-peptide interface
ISSN:	1672-0229, 2210-3244, 2210-3244
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Shrnutí:	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. PepBind is freely accessible at http://pepbind.bicpu.edu.in/.
Bibliografie:	Peptide-binding proteinsdatabase;PepBind;Protein-peptide complex;Protein-peptide interface;Protein-peptide interactiontool;Protein inter-chaininteraction 11-4926/Q 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 signal- ing 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 （Pep- Bind） is a curated and searchable repository of the structures, sequences and experimental observa- tions of 3100 protein~eptide complexes. The web interface contains a computational tool, protein inter-chain interaction （PICI）, for computing several types of weak or strong interactions at the pro- tein peptide interaction interface and visualizing the identified interactions between residues in Jmol viewer. This initial database release focuses on providing protein-peptide interface informa- tion 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. PepBind is freely accessible at http：// pepbind.bicpu.edu.in/. http://dx.doi.org/10.1016/j.gpb.2013.03.002 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1672-0229 2210-3244 2210-3244
DOI:	10.1016/j.gpb.2013.03.002