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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Bibliographic Details
Published in:Genomics, proteomics & bioinformatics Vol. 11; no. 4; pp. 241 - 246
Main Authors: Das, Arindam Atanu, Sharma, Om Prakash, Kumar, Muthuvel Suresh, Krishna, Ramadas, Mathur, Premendu P.
Format: Journal Article
Language:English
Published: 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
Subjects:
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
Online Access:Get full text
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Summary: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/.
Bibliography: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
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ISSN:1672-0229
2210-3244
2210-3244
DOI:10.1016/j.gpb.2013.03.002