Simultaneous Assignment and Structure Determination of Proteins From Sparsely Labeled NMR Datasets

Sparsely labeled NMR samples provide opportunities to study larger biomolecular assemblies than is traditionally done by NMR. This requires new computational tools that can handle the sparsity and ambiguity in the NMR datasets. The MELD (modeling employing limited data) Bayesian approach was assesse...

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Autores principales:	Arup Mondal, Alberto Perez
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	molecular dynamics protein structure determination sparse NMR MELD REMD Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/fd9a73d1ecfb4c3b8cda2e243b79ebe9
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id	oai:doaj.org-article:fd9a73d1ecfb4c3b8cda2e243b79ebe9
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spelling	oai:doaj.org-article:fd9a73d1ecfb4c3b8cda2e243b79ebe92021-12-01T14:09:39ZSimultaneous Assignment and Structure Determination of Proteins From Sparsely Labeled NMR Datasets2296-889X10.3389/fmolb.2021.774394https://doaj.org/article/fd9a73d1ecfb4c3b8cda2e243b79ebe92021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fmolb.2021.774394/fullhttps://doaj.org/toc/2296-889XSparsely labeled NMR samples provide opportunities to study larger biomolecular assemblies than is traditionally done by NMR. This requires new computational tools that can handle the sparsity and ambiguity in the NMR datasets. The MELD (modeling employing limited data) Bayesian approach was assessed to be the best performing in predicting structures from sparsely labeled NMR data in the 13th edition of the Critical Assessment of Structure Prediction (CASP) event—and limitations of the methodology were also noted. In this report, we evaluate the nature and difficulty in modeling unassigned sparsely labeled NMR datasets and report on an improved methodological pipeline leading to higher-accuracy predictions. We benchmark our methodology against the NMR datasets provided by CASP 13.Arup MondalAlberto PerezFrontiers Media S.A.articlemolecular dynamicsprotein structure determinationsparse NMRMELDREMDBiology (General)QH301-705.5ENFrontiers in Molecular Biosciences, Vol 8 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	molecular dynamics protein structure determination sparse NMR MELD REMD Biology (General) QH301-705.5
spellingShingle	molecular dynamics protein structure determination sparse NMR MELD REMD Biology (General) QH301-705.5 Arup Mondal Alberto Perez Simultaneous Assignment and Structure Determination of Proteins From Sparsely Labeled NMR Datasets
description	Sparsely labeled NMR samples provide opportunities to study larger biomolecular assemblies than is traditionally done by NMR. This requires new computational tools that can handle the sparsity and ambiguity in the NMR datasets. The MELD (modeling employing limited data) Bayesian approach was assessed to be the best performing in predicting structures from sparsely labeled NMR data in the 13th edition of the Critical Assessment of Structure Prediction (CASP) event—and limitations of the methodology were also noted. In this report, we evaluate the nature and difficulty in modeling unassigned sparsely labeled NMR datasets and report on an improved methodological pipeline leading to higher-accuracy predictions. We benchmark our methodology against the NMR datasets provided by CASP 13.
format	article
author	Arup Mondal Alberto Perez
author_facet	Arup Mondal Alberto Perez
author_sort	Arup Mondal
title	Simultaneous Assignment and Structure Determination of Proteins From Sparsely Labeled NMR Datasets
title_short	Simultaneous Assignment and Structure Determination of Proteins From Sparsely Labeled NMR Datasets
title_full	Simultaneous Assignment and Structure Determination of Proteins From Sparsely Labeled NMR Datasets
title_fullStr	Simultaneous Assignment and Structure Determination of Proteins From Sparsely Labeled NMR Datasets
title_full_unstemmed	Simultaneous Assignment and Structure Determination of Proteins From Sparsely Labeled NMR Datasets
title_sort	simultaneous assignment and structure determination of proteins from sparsely labeled nmr datasets
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/fd9a73d1ecfb4c3b8cda2e243b79ebe9
work_keys_str_mv	AT arupmondal simultaneousassignmentandstructuredeterminationofproteinsfromsparselylabelednmrdatasets AT albertoperez simultaneousassignmentandstructuredeterminationofproteinsfromsparselylabelednmrdatasets
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Simultaneous Assignment and Structure Determination of Proteins From Sparsely Labeled NMR Datasets

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