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Comparison of non-sequential sets of protein residues

Paper ID Volume ID Publish Year Pages File Format Full-Text
14928 1362 2016 16 PDF Available
Title
Comparison of non-sequential sets of protein residues
Abstract

•The vast majority of binding sites for small ligands are shown to be set of sparsely distributed amino-acids.•A method for the comparison of non-sequential protein segments based on a genetic algorithm is introduced.•The sequence-independent method presented is shown to be better suited than sequence based approaches for comparing ligand-binding sites.

A methodology for performing sequence-free comparison of functional sites in protein structures is introduced. The method is based on a new notion of similarity among superimposed groups of amino acid residues that evaluates both geometry and physico-chemical properties. The method is specifically designed to handle disconnected and sparsely distributed sets of residues. A genetic algorithm is employed to find the superimposition of protein segments that maximizes their similarity. The method was evaluated by performing an all-to-all comparison on two separate sets of ligand-binding sites, comprising 47 protein-FAD (Flavin-Adenine Dinucleotide) and 64 protein-NAD (Nicotinamide-Adenine Dinucleotide) complexes, and comparing the results with those of an existing sequence-based structural alignment tool (TM-Align). The quality of the two methodologies is judged by the methods’ capacity to, among other, correctly predict the similarities in the protein-ligand contact patterns of each pair of binding sites. The results show that using a sequence-free method significantly improves over the sequence-based one, resulting in 23 significant binding-site homologies being detected by the new method but ignored by the sequence-based one.

Keywords
Structural alignment; Sequence-independent; Structural similarity; FAD; NAD; TM-SITE
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Comparison of non-sequential sets of protein residues
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 61, April 2016, Pages 23–38
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
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Price was $35.95
You save - $31
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