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ProRegIn: A regularity index for the selection of native-like tertiary structures of proteins

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Abstract

Automated protein tertiary structure prediction from sequence information alone remains an elusive goal to computational prescriptions. Dividing the problem into three stages viz. secondary structure prediction, generation of plausible main chain loop dihedrals and side chain dihedral optimization, considerable progress has been achieved in our laboratory (http://www.scfbio-iitd.res.in/bhageerath/index.jsp) and elsewhere for proteins with less than 100 amino acids. As a part of our on-going efforts in this direction and to facilitate tertiary structure selection/rejection in containing the combinatorial explosion of trial structures for a specified amino acid sequence, we describe here a web-enabled tool ProRegIn (Protein Regularity Index) developed based on the regularity in the ϕ, ψ dihedral angles of the amino acids that constitute loop regions. We have analysed the dihedrals in loop regions in a non-redundant dataset of 7351 proteins drawn from the Protein Data Bank and categorized them as helix-like or sheet-like (regular) or irregular. We noticed that the regularity thus defined exceeds 86% for ϕ barring glycine and 70% for ψ for all the amino acid side chains including glycine, compelling us to reexamine the conventional view that loops are irregular regions structurally. The regularity index is presented here as a simple tool that finds its application in protein structure analysis as a discriminatory scoring function for rapid screening before the more compute intensive atomic level energy calculations could be undertaken. The tool is made freely accessible over the internet at www.scfbio-iitd.res.in/software/proregin.jsp.

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Authors and Affiliations

  1. Department of Chemistry and Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110 016, India

    Lipi Thukral, Sandhya R Shenoy, Kumkum Bhushan & B Jayaram

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  1. Lipi Thukral
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  2. Sandhya R Shenoy
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  3. Kumkum Bhushan
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  4. B Jayaram
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Correspondence to B Jayaram.

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Supplementary Data pertaining to this article is available on the Journal of Biosciences Website at http://www.ias.ac.in/jbiosci/jan2007/pp71-81-suppl.pdf

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Thukral, L., Shenoy, S.R., Bhushan, K. et al. ProRegIn: A regularity index for the selection of native-like tertiary structures of proteins. J Biosci 32, 71–81 (2007). https://doi.org/10.1007/s12038-007-0007-2

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