PMID: 11933065Apr 5, 2002Paper

Threading with chemostructural restrictions method for predicting fold and functionally significant residues: application to dipeptidylpeptidase IV (DPP-IV)

Proteins
Boris RevaSid Topiol

Abstract

We present a new method for more accurate modeling of protein structure, called threading with chemostructural restrictions. This method addresses those cases in which a target sequence has only remote homologues of known structure for which sequence comparison methods cannot provide accurate alignments. Although remote homologues cannot provide an accurate model for the whole chain, they can be used in constructing practically useful models for the most conserved-and often the most interesting-part of the structure. For many proteins of interest, one can suggest certain chemostructural patterns for the native structure based on the available information on the structural superfamily of the protein, the type of activity, the sequence location of the functionally significant residues, and other factors. We use such patterns to restrict (1) a number of possible templates, and (2) a number of allowed chain conformations on a template. The latter restrictions are imposed in the form of additional template potentials (including terms acting as sequence anchors) that act on certain residues. This approach is tested on remote homologues of alpha/beta-hydrolases that have significant structural similarity in the positions of their cata...Continue Reading

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Citations

Jul 31, 2003·Journal of Molecular Biology·Jaap Willem BackChris G de Koster
Aug 22, 2003·Protein Science : a Publication of the Protein Society·Sharon Goldsmith-Fischman, Barry Honig
May 30, 2006·Protein Science : a Publication of the Protein Society·Richard B JacobsenJoseph S Schoeniger
Jun 4, 2004·The Journal of Biological Chemistry·Jais R BjelkeHanne B Rasmussen
Aug 2, 2003·Critical Reviews in Clinical Laboratory Sciences·Anne-Marie LambeirIngrid De Meester
May 7, 2019·Journal of Bioinformatics and Computational Biology·Ashish Runthala, Shibasish Chowdhury

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