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Exploration of freely available web-interfaces for comparative homology modelling of microbial proteins.

ABSTRACT: AIM:This study was conducted to find the best suited freely available software for modelling of proteins by taking a few sample proteins. The proteins used were small to big in size with available crystal structures for the purpose of benchmarking. Key players like Phyre2, Swiss-Model, CPHmodels-3.0, Homer, (PS)2, (PS)(2)-V(2), Modweb were used for the comparison and model generation. RESULTS:Benchmarking process was done for four proteins, Icl, InhA, and KatG of Mycobacterium tuberculosis and RpoB of Thermus Thermophilus to get the most suited software. Parameters compared during analysis gave relatively better values for Phyre2 and Swiss-Model. CONCLUSION:This comparative study gave the information that Phyre2 and Swiss-Model make good models of small and large proteins as compared to other screened software. Other software was also good but is often not very efficient in providing full-length and properly folded structure.

SUBMITTER: Nema V

PROVIDER: S-EPMC3766314 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Exploration of freely available web-interfaces for comparative homology modelling of microbial proteins.

Nema Vijay V Pal Sudhir Kumar SK

Bioinformation 20130828 15

<h4>Aim</h4>This study was conducted to find the best suited freely available software for modelling of proteins by taking a few sample proteins. The proteins used were small to big in size with available crystal structures for the purpose of benchmarking. Key players like Phyre2, Swiss-Model, CPHmodels-3.0, Homer, (PS)2, (PS)(2)-V(2), Modweb were used for the comparison and model generation.<h4>Results</h4>Benchmarking process was done for four proteins, Icl, InhA, and KatG of Mycobacterium tub ...[more]

PMID: 24023424

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Exploration of freely available web-interfaces for comparative homology modelling of microbial proteins.

Publications

Exploration of freely available web-interfaces for comparative homology modelling of microbial proteins.

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