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

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A homology/ab initio hybrid algorithm for sampling near-native protein conformations.

Priyanka Dhingra¹, Bhyravabhotla Jayaram

¹Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India.

Journal of Computational Chemistry

|June 4, 2013

Summary

A new hybrid algorithm, Bhageerath-H Strgen, improves protein tertiary structure prediction by enhancing conformational sampling. It efficiently generates near-native protein structures using homology and ab initio methods.

Keywords:

ab initio modeling fold recognition homology modeling loop modeling protein folding protein tertiary structure prediction

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Published on: July 14, 2015

Area of Science:

Computational Biology
Structural Bioinformatics
Protein Structure Prediction

Background:

Protein tertiary structure prediction is crucial for understanding protein function.
Current conformational sampling algorithms face challenges in efficiently searching protein fold space.
Integrating homology, fold recognition, and ab initio methods can improve prediction accuracy.

Purpose of the Study:

To develop Bhageerath-H Strgen, a hybrid algorithm for enhanced protein conformational sampling.
To improve the generation of near-native protein conformations.
To provide a web-accessible tool for protein decoy generation.

Main Methods:

Developed Bhageerath-H Strgen, a homology/ab initio hybrid algorithm.
Tested the algorithm on the CASP9 dataset comprising 116 protein targets.
Evaluated the efficiency and performance against other decoy generation methods.

Main Results:

Bhageerath-H Strgen generated structures with a TM-score ≥ 0.5 in 93% of tested cases.
The algorithm demonstrated efficient performance compared to existing decoy generation methods.
A web tool for Bhageerath-H Strgen is now freely accessible.

Conclusions:

Bhageerath-H Strgen effectively enhances protein conformational sampling.
The hybrid approach offers an efficient strategy for generating near-native protein structures.
The web tool facilitates broader access to advanced protein decoy generation capabilities.