Comparative Study of Homology Based Structure Prediction and Structure Validation Tools on Some Proteins from the bhlh family.

Tanvee Ajit Pardeshi, Akhil Jobby, Sameer Chaudhary

Abstract


Comparative homology modeling has become an efficient and easy method for predicting the unknown three dimensional structure of a protein based on sequence alignment. The steps involved are template alignment, loop assignment, model building and model refinement. However, it was noticed that though the basic steps for modeling the protein was same, the results produced by different tools that is available varied, possibly due to the efficiency of the algorithm and other factors. Here, five homology modelling tools were used to compare the results for some proteins of the bhlh family. It was also noticed that structure validation tools had different results. To compare the results ProcheckRamchandran plot from PDBSum Generate and Ramchandran plot from SPDBV were used. The differing results were compared using simple statistical approach and the inference was obtained as patterns for the tools.

Keywords


bhlh proteins; Homology Modeling; protein structure prediction; Structure Validation;

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References


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