Recommendations of the wwPDB NMR Validation Task Force
As methods for analysis of biomolecular structure and dynamics using nuclear magnetic resonance spectroscopy (NMR) continue to advance, the resulting 3D structures, chemical shifts, and other NMR data are broadly impacting biology, chemistry, and medicine. Structure model assessment is a critical ar...
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Veröffentlicht in: | Structure (London) 2013-09, Vol.21 (9), p.1563-1570 |
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creator | Montelione, Gaetano T. Nilges, Michael Bax, Ad Güntert, Peter Herrmann, Torsten Richardson, Jane S. Schwieters, Charles D. Vranken, Wim F. Vuister, Geerten W. Wishart, David S. Berman, Helen M. Kleywegt, Gerard J. Markley, John L. |
description | As methods for analysis of biomolecular structure and dynamics using nuclear magnetic resonance spectroscopy (NMR) continue to advance, the resulting 3D structures, chemical shifts, and other NMR data are broadly impacting biology, chemistry, and medicine. Structure model assessment is a critical area of NMR methods development, and is an essential component of the process of making these structures accessible and useful to the wider scientific community. For these reasons, the Worldwide Protein Data Bank (wwPDB) has convened an NMR Validation Task Force (NMR-VTF) to work with wwPDB partners in developing metrics and policies for biomolecular NMR data harvesting, structure representation, and structure quality assessment. This paper summarizes the recommendations of the NMR-VTF, and lays the groundwork for future work in developing standards and metrics for biomolecular NMR structure quality assessment.
•Well-developed methods can form a basis for standardized NMR structure assessment•Tools for validation of X-ray crystal structures are appropriate for NMR structures•NMR structure validation is generally applicable only to “well-defined” regions•Further research is required to address key issues of NMR structure validation
As analyses of biomolecular structure and dynamics by nuclear magnetic resonance (NMR) spectroscopy continue to advance, the resulting structures have a broad impact. Montelione et al. summarize recommendations for developing metrics and policies for biomolecular NMR structure representation and validation. |
doi_str_mv | 10.1016/j.str.2013.07.021 |
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•Well-developed methods can form a basis for standardized NMR structure assessment•Tools for validation of X-ray crystal structures are appropriate for NMR structures•NMR structure validation is generally applicable only to “well-defined” regions•Further research is required to address key issues of NMR structure validation
As analyses of biomolecular structure and dynamics by nuclear magnetic resonance (NMR) spectroscopy continue to advance, the resulting structures have a broad impact. Montelione et al. summarize recommendations for developing metrics and policies for biomolecular NMR structure representation and validation.</description><identifier>ISSN: 0969-2126</identifier><identifier>EISSN: 1878-4186</identifier><identifier>DOI: 10.1016/j.str.2013.07.021</identifier><identifier>PMID: 24010715</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Accessibility ; Advisory Committees ; Analytical chemistry ; Assessments ; Chemical Sciences ; Databases, Protein - standards ; Guidelines as Topic ; Knowledge Bases ; Models, Molecular ; Nuclear magnetic resonance ; Nuclear Magnetic Resonance, Biomolecular ; Policies ; Protein Conformation ; Proteins - chemistry ; Quality assessment ; Quality Control ; Reference Standards ; Tasks ; Three dimensional ; Validation Studies as Topic</subject><ispartof>Structure (London), 2013-09, Vol.21 (9), p.1563-1570</ispartof><rights>2013 Elsevier Ltd</rights><rights>Copyright © 2013 Elsevier Ltd. All rights reserved.</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><rights>2013 Elsevier Inc. All rights reserved. 2013</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c584t-ea29667650c999220f5b594a4a35b2e59db0b56204c97678194e967a9e8ac2e13</citedby><cites>FETCH-LOGICAL-c584t-ea29667650c999220f5b594a4a35b2e59db0b56204c97678194e967a9e8ac2e13</cites><orcidid>0000-0002-1451-8092 ; 0000-0003-2115-4781</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0969212613002712$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>230,314,776,780,881,3537,27901,27902,65306</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24010715$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-00955839$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Montelione, Gaetano T.</creatorcontrib><creatorcontrib>Nilges, Michael</creatorcontrib><creatorcontrib>Bax, Ad</creatorcontrib><creatorcontrib>Güntert, Peter</creatorcontrib><creatorcontrib>Herrmann, Torsten</creatorcontrib><creatorcontrib>Richardson, Jane S.</creatorcontrib><creatorcontrib>Schwieters, Charles D.</creatorcontrib><creatorcontrib>Vranken, Wim F.</creatorcontrib><creatorcontrib>Vuister, Geerten W.</creatorcontrib><creatorcontrib>Wishart, David S.</creatorcontrib><creatorcontrib>Berman, Helen M.</creatorcontrib><creatorcontrib>Kleywegt, Gerard J.</creatorcontrib><creatorcontrib>Markley, John L.</creatorcontrib><title>Recommendations of the wwPDB NMR Validation Task Force</title><title>Structure (London)</title><addtitle>Structure</addtitle><description>As methods for analysis of biomolecular structure and dynamics using nuclear magnetic resonance spectroscopy (NMR) continue to advance, the resulting 3D structures, chemical shifts, and other NMR data are broadly impacting biology, chemistry, and medicine. Structure model assessment is a critical area of NMR methods development, and is an essential component of the process of making these structures accessible and useful to the wider scientific community. For these reasons, the Worldwide Protein Data Bank (wwPDB) has convened an NMR Validation Task Force (NMR-VTF) to work with wwPDB partners in developing metrics and policies for biomolecular NMR data harvesting, structure representation, and structure quality assessment. This paper summarizes the recommendations of the NMR-VTF, and lays the groundwork for future work in developing standards and metrics for biomolecular NMR structure quality assessment.
•Well-developed methods can form a basis for standardized NMR structure assessment•Tools for validation of X-ray crystal structures are appropriate for NMR structures•NMR structure validation is generally applicable only to “well-defined” regions•Further research is required to address key issues of NMR structure validation
As analyses of biomolecular structure and dynamics by nuclear magnetic resonance (NMR) spectroscopy continue to advance, the resulting structures have a broad impact. Montelione et al. summarize recommendations for developing metrics and policies for biomolecular NMR structure representation and validation.</description><subject>Accessibility</subject><subject>Advisory Committees</subject><subject>Analytical chemistry</subject><subject>Assessments</subject><subject>Chemical Sciences</subject><subject>Databases, Protein - standards</subject><subject>Guidelines as Topic</subject><subject>Knowledge Bases</subject><subject>Models, Molecular</subject><subject>Nuclear magnetic resonance</subject><subject>Nuclear Magnetic Resonance, Biomolecular</subject><subject>Policies</subject><subject>Protein Conformation</subject><subject>Proteins - chemistry</subject><subject>Quality assessment</subject><subject>Quality Control</subject><subject>Reference Standards</subject><subject>Tasks</subject><subject>Three dimensional</subject><subject>Validation Studies as Topic</subject><issn>0969-2126</issn><issn>1878-4186</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkU1v1DAQhi0EokvhB3BBOcIh6djxp5CQSqEt0vKhqnC1HGeW9ZLExc5uxb8nq5Sq5YA4jTTzvu-M_RDynEJFgcqjTZXHVDGgdQWqAkYfkAXVSpecavmQLMBIUzLK5AF5kvMGAJgAeEwOGAcKiooFkRfoY9_j0LoxxCEXcVWMayyur7-8e1t8-nhRfHNdmIfFpcs_itOYPD4lj1auy_jsph6Sr6fvL0_Oy-Xnsw8nx8vSC83HEh0zUiopwBtjGIOVaIThjrtaNAyFaRtohGTAvVFSaWo4GqmcQe08Q1ofkjdz7tW26bH1OIzJdfYqhd6lXza6YO9PhrC23-PO1lpzUGoKeDUHrP-ynR8v7b4HYITQtdntl728WZbizy3m0fYhe-w6N2DcZkuFVKAkp_8h5TVlRgstJymdpT7FnBOubs-gYPcY7cZOGO0eowVlJ4yT58XdZ986_nCbBK9nAU6fvwuYbPYBB49tSOhH28bwj_jf1bWqxA</recordid><startdate>20130903</startdate><enddate>20130903</enddate><creator>Montelione, Gaetano T.</creator><creator>Nilges, Michael</creator><creator>Bax, Ad</creator><creator>Güntert, Peter</creator><creator>Herrmann, Torsten</creator><creator>Richardson, Jane S.</creator><creator>Schwieters, Charles D.</creator><creator>Vranken, Wim F.</creator><creator>Vuister, Geerten W.</creator><creator>Wishart, David S.</creator><creator>Berman, Helen M.</creator><creator>Kleywegt, Gerard J.</creator><creator>Markley, John L.</creator><general>Elsevier Inc</general><general>Elsevier (Cell Press)</general><scope>6I.</scope><scope>AAFTH</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7U5</scope><scope>8FD</scope><scope>F28</scope><scope>FR3</scope><scope>L7M</scope><scope>1XC</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-1451-8092</orcidid><orcidid>https://orcid.org/0000-0003-2115-4781</orcidid></search><sort><creationdate>20130903</creationdate><title>Recommendations of the wwPDB NMR Validation Task Force</title><author>Montelione, Gaetano T. ; Nilges, Michael ; Bax, Ad ; Güntert, Peter ; Herrmann, Torsten ; Richardson, Jane S. ; Schwieters, Charles D. ; Vranken, Wim F. ; Vuister, Geerten W. ; Wishart, David S. ; Berman, Helen M. ; Kleywegt, Gerard J. ; Markley, John L.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c584t-ea29667650c999220f5b594a4a35b2e59db0b56204c97678194e967a9e8ac2e13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Accessibility</topic><topic>Advisory Committees</topic><topic>Analytical chemistry</topic><topic>Assessments</topic><topic>Chemical Sciences</topic><topic>Databases, Protein - standards</topic><topic>Guidelines as Topic</topic><topic>Knowledge Bases</topic><topic>Models, Molecular</topic><topic>Nuclear magnetic resonance</topic><topic>Nuclear Magnetic Resonance, Biomolecular</topic><topic>Policies</topic><topic>Protein Conformation</topic><topic>Proteins - chemistry</topic><topic>Quality assessment</topic><topic>Quality Control</topic><topic>Reference Standards</topic><topic>Tasks</topic><topic>Three dimensional</topic><topic>Validation Studies as Topic</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Montelione, Gaetano T.</creatorcontrib><creatorcontrib>Nilges, Michael</creatorcontrib><creatorcontrib>Bax, Ad</creatorcontrib><creatorcontrib>Güntert, Peter</creatorcontrib><creatorcontrib>Herrmann, Torsten</creatorcontrib><creatorcontrib>Richardson, Jane S.</creatorcontrib><creatorcontrib>Schwieters, Charles D.</creatorcontrib><creatorcontrib>Vranken, Wim F.</creatorcontrib><creatorcontrib>Vuister, Geerten W.</creatorcontrib><creatorcontrib>Wishart, David S.</creatorcontrib><creatorcontrib>Berman, Helen M.</creatorcontrib><creatorcontrib>Kleywegt, Gerard J.</creatorcontrib><creatorcontrib>Markley, John L.</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>Technology Research Database</collection><collection>ANTE: Abstracts in New Technology & Engineering</collection><collection>Engineering Research Database</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Structure (London)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Montelione, Gaetano T.</au><au>Nilges, Michael</au><au>Bax, Ad</au><au>Güntert, Peter</au><au>Herrmann, Torsten</au><au>Richardson, Jane S.</au><au>Schwieters, Charles D.</au><au>Vranken, Wim F.</au><au>Vuister, Geerten W.</au><au>Wishart, David S.</au><au>Berman, Helen M.</au><au>Kleywegt, Gerard J.</au><au>Markley, John L.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Recommendations of the wwPDB NMR Validation Task Force</atitle><jtitle>Structure (London)</jtitle><addtitle>Structure</addtitle><date>2013-09-03</date><risdate>2013</risdate><volume>21</volume><issue>9</issue><spage>1563</spage><epage>1570</epage><pages>1563-1570</pages><issn>0969-2126</issn><eissn>1878-4186</eissn><abstract>As methods for analysis of biomolecular structure and dynamics using nuclear magnetic resonance spectroscopy (NMR) continue to advance, the resulting 3D structures, chemical shifts, and other NMR data are broadly impacting biology, chemistry, and medicine. Structure model assessment is a critical area of NMR methods development, and is an essential component of the process of making these structures accessible and useful to the wider scientific community. For these reasons, the Worldwide Protein Data Bank (wwPDB) has convened an NMR Validation Task Force (NMR-VTF) to work with wwPDB partners in developing metrics and policies for biomolecular NMR data harvesting, structure representation, and structure quality assessment. This paper summarizes the recommendations of the NMR-VTF, and lays the groundwork for future work in developing standards and metrics for biomolecular NMR structure quality assessment.
•Well-developed methods can form a basis for standardized NMR structure assessment•Tools for validation of X-ray crystal structures are appropriate for NMR structures•NMR structure validation is generally applicable only to “well-defined” regions•Further research is required to address key issues of NMR structure validation
As analyses of biomolecular structure and dynamics by nuclear magnetic resonance (NMR) spectroscopy continue to advance, the resulting structures have a broad impact. Montelione et al. summarize recommendations for developing metrics and policies for biomolecular NMR structure representation and validation.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>24010715</pmid><doi>10.1016/j.str.2013.07.021</doi><tpages>8</tpages><orcidid>https://orcid.org/0000-0002-1451-8092</orcidid><orcidid>https://orcid.org/0000-0003-2115-4781</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Accessibility Advisory Committees Analytical chemistry Assessments Chemical Sciences Databases, Protein - standards Guidelines as Topic Knowledge Bases Models, Molecular Nuclear magnetic resonance Nuclear Magnetic Resonance, Biomolecular Policies Protein Conformation Proteins - chemistry Quality assessment Quality Control Reference Standards Tasks Three dimensional Validation Studies as Topic |
title | Recommendations of the wwPDB NMR Validation Task Force |
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