Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment

Genome-wide protein structure prediction and structure-based function annotation have been a long-term goal in molecular biology but not yet become possible due to difficulties in modeling distant-homology targets. We developed a hybrid pipeline combining ab initio folding and template-based modelin...

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Main Authors:	Xu, Dong, Zhang, Yang
Format:	Online
Language:	English
Published:	Nature Publishing Group 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3667494/

id	pubmed-3667494
recordtype	oai_dc
spelling	pubmed-36674942013-05-30 Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment Xu, Dong Zhang, Yang Article Genome-wide protein structure prediction and structure-based function annotation have been a long-term goal in molecular biology but not yet become possible due to difficulties in modeling distant-homology targets. We developed a hybrid pipeline combining ab initio folding and template-based modeling for genome-wide structure prediction applied to the Escherichia coli genome. The pipeline was tested on 43 known sequences, where QUARK-based ab initio folding simulation generated models with TM-score 17% higher than that by traditional comparative modeling methods. For 495 unknown hard sequences, 72 are predicted to have a correct fold (TM-score > 0.5) and 321 have a substantial portion of structure correctly modeled (TM-score > 0.35). 317 sequences can be reliably assigned to a SCOP fold family based on structural analogy to existing proteins in PDB. The presented results, as a case study of E. coli, represent promising progress towards genome-wide structure modeling and fold family assignment using state-of-the-art ab initio folding algorithms. Nature Publishing Group 2013-05-30 /pmc/articles/PMC3667494/ /pubmed/23719418 http://dx.doi.org/10.1038/srep01895 Text en Copyright © 2013, Macmillan Publishers Limited. All rights reserved http://creativecommons.org/licenses/by-nc-nd/3.0/ This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/3.0/
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Xu, Dong Zhang, Yang
spellingShingle	Xu, Dong Zhang, Yang Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment
author_facet	Xu, Dong Zhang, Yang
author_sort	Xu, Dong
title	Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment
title_short	Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment
title_full	Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment
title_fullStr	Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment
title_full_unstemmed	Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment
title_sort	ab initio structure prediction for escherichia coli: towards genome-wide protein structure modeling and fold assignment
description	Genome-wide protein structure prediction and structure-based function annotation have been a long-term goal in molecular biology but not yet become possible due to difficulties in modeling distant-homology targets. We developed a hybrid pipeline combining ab initio folding and template-based modeling for genome-wide structure prediction applied to the Escherichia coli genome. The pipeline was tested on 43 known sequences, where QUARK-based ab initio folding simulation generated models with TM-score 17% higher than that by traditional comparative modeling methods. For 495 unknown hard sequences, 72 are predicted to have a correct fold (TM-score > 0.5) and 321 have a substantial portion of structure correctly modeled (TM-score > 0.35). 317 sequences can be reliably assigned to a SCOP fold family based on structural analogy to existing proteins in PDB. The presented results, as a case study of E. coli, represent promising progress towards genome-wide structure modeling and fold family assignment using state-of-the-art ab initio folding algorithms.
publisher	Nature Publishing Group
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3667494/
_version_	1611982170381877248

Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment

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