Recognizing protein substructure similarity using segmental threading.

Structure
Sitao Wu, Yang Zhang

Abstract

Protein template identification is essential to protein structure and function predictions. However, conventional whole-chain threading approaches often fail to recognize conserved substructure motifs when the target and templates do not share the same fold. We developed a new approach, SEGMER, for identifying protein substructure similarities by segmental threading. The target sequence is split into segments of two to four consecutive or nonconsecutive secondary structural elements, which are then threaded through PDB to identify appropriate substructure motifs. SEGMER is tested on 144 nonredundant hard proteins. When combined with whole-chain threading, the TM-score of alignments and accuracy of spatial restraints of SEGMER increase by 16% and 25%, respectively, compared with that by the whole-chain threading methods only. When tested on 12 free modeling targets from CASP8, SEGMER increases the TM-score and contact accuracy by 28% and 48%, respectively. This significant improvement should have important impact on protein structure modeling and functional inference.

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Citations

Jul 27, 2010·Critical Reviews in Biochemistry and Molecular Biology·James H Hurley
Apr 2, 2016·BioMed Research International·Jose C Jimenez-LopezJuan de Dios Alché
Nov 23, 2011·Proteins·Hongyi Zhou, Jeffrey Skolnick
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Jan 13, 2016·Journal of Cellular Biochemistry·Muhammad Tariq ZahidAbdul Rauf Shakoori
Dec 8, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Leonardo CorreaMarcio Dorn
Mar 19, 2019·Proteins·Sutanu Bhattacharya, Debswapna Bhattacharya
Feb 23, 2020·Scientific Reports·Sutanu Bhattacharya, Debswapna Bhattacharya
May 29, 2021·Frontiers in Molecular Biosciences·Sutanu BhattacharyaDebswapna Bhattacharya

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