PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions
Arindam Atanu Das1, Om Prakash Sharma, Muthuvel Suresh Kumar
1Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry 605014, India.
Genomics, Proteomics & Bioinformatics
|July 31, 2013
Summary
The Peptide Binding Protein Database (PepBind) offers a curated resource for 3100 protein-peptide complexes. It aids researchers in understanding these crucial interactions for cellular signaling and drug design.
Area of Science:
- Biochemistry and Molecular Biology
- Structural Biology
- Bioinformatics
Background:
- Protein-peptide interactions are fundamental to cellular signaling and regulation.
- Understanding these interactions is vital for drug design but often challenging.
- Existing tools and databases can facilitate the study of these complexes.
Purpose of the Study:
- To introduce the Peptide Binding Protein Database (PepBind) as a comprehensive resource for protein-peptide complexes.
- To provide structural, sequential, and experimental data for over 3100 protein-peptide complexes.
- To offer a computational tool for analyzing protein-peptide interaction interfaces.
Main Methods:
- Curated collection and organization of structural and sequence data from the Protein Data Bank (PDB).
- Development of the Peptide Binding Protein Database (PepBind) with a searchable web interface.
- Implementation of the protein inter-chain interaction (PICI) tool for analyzing interface interactions.
- Classification of protein-peptide complexes based on cellular activity.
Main Results:
- PepBind contains data for 3100 protein-peptide complexes.
- The database includes structural, sequence, and experimental information.
- The PICI tool allows for the computation and visualization of interactions at the protein-peptide interface.
- Over 40% of complexes are involved in regulatory pathways, and nearly 20% in the immune system.
Conclusions:
- PepBind serves as a valuable, curated resource for studying protein-peptide interactions.
- The database and its associated tools facilitate research into cellular signaling and regulatory networks.
- Protein-peptide complexes play a significant role in cellular processes, particularly in regulation and immunity.
Related Concept Videos
02:04Protein-protein Interfaces
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
02:04Protein-Protein Interfaces
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
02:47Protein Families
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...