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ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures
R Sabarinathan1, Raunak Basu, K Sekar
1Bioinformatics Centre (Centre of Excellence in Structural Biology and Bio-computing), Indian Institute of Science, Bangalore 560 012, India.
Computational Biology and Chemistry
|May 1, 2010
Summary
Gene duplication leads to similar structural repeats in proteins, forming repeat domains. A new method, ProSTRIP, identifies these structural repeats in 3D protein structures using Calpha angles.
Area of Science:
- Structural biology
- Bioinformatics
- Computational biology
Background:
- Similar structural repeats in proteins arise from gene duplication events.
- These repeats function as building blocks, forming compact structural and functional units known as repeat domains.
- Protein families with these repeats are crucial for protein-protein interactions and ligand binding.
Purpose of the Study:
- To develop a novel computational method for identifying similar structural repeats within protein 3D structures.
- To address the limitations of sequence-based repeat identification for structural analysis.
Main Methods:
- Developed ProSTRIP, a dynamic programming-based method.
- Utilizes protein backbone Calpha angles for repeat detection.
- Implemented as an internet computing server with graphical visualization.
Main Results:
- ProSTRIP successfully identifies similar structural repeats in protein structures.
- The method provides graphical visualization of detected repeats.
- An accessible online server is available for public use.
Conclusions:
- ProSTRIP offers an effective approach for analyzing structural repeats in proteins.
- The method enhances the understanding of protein architecture and function.
- The online server facilitates research in structural bioinformatics.
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