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



Vijay Nema1* & Sudhir Kumar Pal2



1Microbiology and Clinical Pathology, 73, G-Block, MIDC, Bhosari, Pune, Maharashtra-411 026, India; 2Dr. DY Patil University, Plot no.-50, Sector-15, CBD Belapur, Navi Mumbai-400614, India


Email; *Corresponding author


Article Type




Received August 05, 2013; Accepted August 07, 2013; Published August 28, 2013



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-V2, 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.



Mycobacterium tuberculosis, Proteins, Homology modelling, Freeware, Benchmarking.



Nema & Pal, Bioinformation 9(15): 796-801 (2013)


Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.