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An efficient algorithm for protein structure comparison using elastic shape analysis
S Srivastava1, S B Lal2, D C Mishra2
1ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India ; Biostatistics Shared Facility, James Graham Brown Cancer Center, University of Louisville, Louisville, USA.
Algorithms for Molecular Biology : AMB
|October 7, 2016
Summary
A new algorithm efficiently compares protein structures using elastic shape analysis and auxiliary data, reducing computation time by up to 90% without sacrificing accuracy. This method aids in protein function prediction and evolutionary analysis.
Area of Science:
- Computational Biology
- Structural Bioinformatics
- Biophysics
Background:
- Protein structure comparison is crucial for predicting protein function and understanding evolutionary relationships.
- Existing methods for protein structure comparison face limitations in accuracy, computational time, and space complexity.
- There is a need for improved computational efficiency in protein comparison by integrating biological and structural properties.
Purpose of the Study:
- To develop an efficient algorithm for protein structure comparison.
- To enhance computational efficiency without compromising accuracy.
- To incorporate biological and structural properties into protein comparison techniques.
Main Methods:
- Developed an efficient algorithm using elastic shape analysis for protein structure comparison.
- Represented protein structures using square-root velocity functions incorporating 3D atomic coordinates and side-chain properties.
- Employed singular value decomposition for optimal rotation and dynamic programming for optimal matching.
- Utilized geodesic distance to calculate dissimilarity scores between protein structures.
Main Results:
- The developed algorithm demonstrated significantly improved efficiency, reducing running time by 80-90% compared to existing methods.
- Accuracy of protein structure comparison was maintained without compromise.
- Source codes were developed in R, and a user-friendly web application, ProtSComp, was created for free access.
Conclusions:
- The new methodology and algorithm offer substantially reduced computational time for protein structure comparison.
- Accuracy is preserved, demonstrating the effectiveness of incorporating 3D atomic coordinates and residue-wise molecular properties.
- The developed approach provides an efficient and accurate tool for structural bioinformatics and functional prediction.
