NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB

For many macromolecular NMR ensembles from the Protein Data Bank (PDB) the experiment-based restraint lists are available, while other experimental data, mainly chemical shift values, are often available from the BioMagResBank. The accuracy and precision of the coordinates in these macromolecular NM...

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Main Authors:	Doreleijers, Jurgen F., Vranken, Wim F., Schulte, Christopher, Markley, John L., Ulrich, Eldon L., Vriend, Gert, Vuister, Geerten W.
Format:	Online
Language:	English
Published:	Oxford University Press 2012
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245154/

id	pubmed-3245154
recordtype	oai_dc
spelling	pubmed-32451542012-01-10 NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB Doreleijers, Jurgen F. Vranken, Wim F. Schulte, Christopher Markley, John L. Ulrich, Eldon L. Vriend, Gert Vuister, Geerten W. Articles For many macromolecular NMR ensembles from the Protein Data Bank (PDB) the experiment-based restraint lists are available, while other experimental data, mainly chemical shift values, are often available from the BioMagResBank. The accuracy and precision of the coordinates in these macromolecular NMR ensembles can be improved by recalculation using the available experimental data and present-day software. Such efforts, however, generally fail on half of all NMR ensembles due to the syntactic and semantic heterogeneity of the underlying data and the wide variety of formats used for their deposition. We have combined the remediated restraint information from our NMR Restraints Grid (NRG) database with available chemical shifts from the BioMagResBank and the Common Interface for NMR structure Generation (CING) structure validation reports into the weekly updated NRG-CING database (http://nmr.cmbi.ru.nl/NRG-CING). Eleven programs have been included in the NRG-CING production pipeline to arrive at validation reports that list for each entry the potential inconsistencies between the coordinates and the available experimental NMR data. The longitudinal validation of these data in a publicly available relational database yields a set of indicators that can be used to judge the quality of every macromolecular structure solved with NMR. The remediated NMR experimental data sets and validation reports are freely available online. Oxford University Press 2012-01 2011-12-01 /pmc/articles/PMC3245154/ /pubmed/22139937 http://dx.doi.org/10.1093/nar/gkr1134 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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	Doreleijers, Jurgen F. Vranken, Wim F. Schulte, Christopher Markley, John L. Ulrich, Eldon L. Vriend, Gert Vuister, Geerten W.
spellingShingle	Doreleijers, Jurgen F. Vranken, Wim F. Schulte, Christopher Markley, John L. Ulrich, Eldon L. Vriend, Gert Vuister, Geerten W. NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB
author_facet	Doreleijers, Jurgen F. Vranken, Wim F. Schulte, Christopher Markley, John L. Ulrich, Eldon L. Vriend, Gert Vuister, Geerten W.
author_sort	Doreleijers, Jurgen F.
title	NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB
title_short	NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB
title_full	NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB
title_fullStr	NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB
title_full_unstemmed	NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB
title_sort	nrg-cing: integrated validation reports of remediated experimental biomolecular nmr data and coordinates in wwpdb
description	For many macromolecular NMR ensembles from the Protein Data Bank (PDB) the experiment-based restraint lists are available, while other experimental data, mainly chemical shift values, are often available from the BioMagResBank. The accuracy and precision of the coordinates in these macromolecular NMR ensembles can be improved by recalculation using the available experimental data and present-day software. Such efforts, however, generally fail on half of all NMR ensembles due to the syntactic and semantic heterogeneity of the underlying data and the wide variety of formats used for their deposition. We have combined the remediated restraint information from our NMR Restraints Grid (NRG) database with available chemical shifts from the BioMagResBank and the Common Interface for NMR structure Generation (CING) structure validation reports into the weekly updated NRG-CING database (http://nmr.cmbi.ru.nl/NRG-CING). Eleven programs have been included in the NRG-CING production pipeline to arrive at validation reports that list for each entry the potential inconsistencies between the coordinates and the available experimental NMR data. The longitudinal validation of these data in a publicly available relational database yields a set of indicators that can be used to judge the quality of every macromolecular structure solved with NMR. The remediated NMR experimental data sets and validation reports are freely available online.
publisher	Oxford University Press
publishDate	2012
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245154/
_version_	1611496272877846528

NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB

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