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Updated: Mar 14, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

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

This summary is machine-generated.

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.

Keywords:

Backbone atoms Geodesic distance Protein structure comparison Side chain properties

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Last Updated: Mar 14, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Published on: July 16, 2017

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

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.