A simple method based on multiple alignment and phylogeny to derive a correlation between the protein fold and sequence via motif search

Interdisciplinary Sciences, Computational Life Sciences
Syed Baquer RizviVikash Kumar Dubey

Abstract

Predicting information regarding the structure of the protein from its sequence still remains an uphill task. Though both are intimately linked, it has been found difficult so far to get a direct correlation between the two. In our present approach we use a simple method based on multiple alignment and phylogeny to derive a correlation between the protein structure and sequence via motif search. The protein families which we have considered are SH2 like, Homeodomain, Leucine rich repeat, Alphabeta knot trefoilknot and ferritin like helix bundle. We have been able to successfully predict the protein families with an average prediction of accuracy of 81%, the highest being 89% and the lowest being 73% on our test data set.

References

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Jan 18, 2005·Proceedings of the National Academy of Sciences of the United States of America·Yang Zhang, Jeffrey Skolnick
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Citations

Jun 16, 2011·BMC Structural Biology·Felipe VillaneloOctavio Monasterio
May 2, 2014·Nucleic Acids Research·Erik S HopmansHanlee P Ji

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