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CING: an integrated residue-based structure validation program suite

We present a suite of programs, named CING for Common Interface for NMR Structure Generation that provides for a residue-based, integrated validation of the structural NMR ensemble in conjunction with the experimental restraints and other input data. External validation programs and new internal val...

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Autores principales: Doreleijers, Jurgen F., Sousa da Silva, Alan W., Krieger, Elmar, Nabuurs, Sander B., Spronk, Christian A. E. M., Stevens, Tim J., Vranken, Wim F., Vriend, Gert, Vuister, Geerten W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Netherlands 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3483101/
https://www.ncbi.nlm.nih.gov/pubmed/22986687
http://dx.doi.org/10.1007/s10858-012-9669-7
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author Doreleijers, Jurgen F.
Sousa da Silva, Alan W.
Krieger, Elmar
Nabuurs, Sander B.
Spronk, Christian A. E. M.
Stevens, Tim J.
Vranken, Wim F.
Vriend, Gert
Vuister, Geerten W.
author_facet Doreleijers, Jurgen F.
Sousa da Silva, Alan W.
Krieger, Elmar
Nabuurs, Sander B.
Spronk, Christian A. E. M.
Stevens, Tim J.
Vranken, Wim F.
Vriend, Gert
Vuister, Geerten W.
author_sort Doreleijers, Jurgen F.
collection PubMed
description We present a suite of programs, named CING for Common Interface for NMR Structure Generation that provides for a residue-based, integrated validation of the structural NMR ensemble in conjunction with the experimental restraints and other input data. External validation programs and new internal validation routines compare the NMR-derived models with empirical data, measured chemical shifts, distance- and dihedral restraints and the results are visualized in a dynamic Web 2.0 report. A red–orange–green score is used for residues and restraints to direct the user to those critiques that warrant further investigation. Overall green scores below ~20 % accompanied by red scores over ~50 % are strongly indicative of poorly modelled structures. The publically accessible, secure iCing webserver (https://nmr.le.ac.uk) allows individual users to upload the NMR data and run a CING validation analysis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10858-012-9669-7) contains supplementary material, which is available to authorized users.
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spelling pubmed-34831012012-11-05 CING: an integrated residue-based structure validation program suite Doreleijers, Jurgen F. Sousa da Silva, Alan W. Krieger, Elmar Nabuurs, Sander B. Spronk, Christian A. E. M. Stevens, Tim J. Vranken, Wim F. Vriend, Gert Vuister, Geerten W. J Biomol NMR Article We present a suite of programs, named CING for Common Interface for NMR Structure Generation that provides for a residue-based, integrated validation of the structural NMR ensemble in conjunction with the experimental restraints and other input data. External validation programs and new internal validation routines compare the NMR-derived models with empirical data, measured chemical shifts, distance- and dihedral restraints and the results are visualized in a dynamic Web 2.0 report. A red–orange–green score is used for residues and restraints to direct the user to those critiques that warrant further investigation. Overall green scores below ~20 % accompanied by red scores over ~50 % are strongly indicative of poorly modelled structures. The publically accessible, secure iCing webserver (https://nmr.le.ac.uk) allows individual users to upload the NMR data and run a CING validation analysis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10858-012-9669-7) contains supplementary material, which is available to authorized users. Springer Netherlands 2012-09-18 2012 /pmc/articles/PMC3483101/ /pubmed/22986687 http://dx.doi.org/10.1007/s10858-012-9669-7 Text en © The Author(s) 2012 https://creativecommons.org/licenses/by/4.0/ This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.
spellingShingle Article
Doreleijers, Jurgen F.
Sousa da Silva, Alan W.
Krieger, Elmar
Nabuurs, Sander B.
Spronk, Christian A. E. M.
Stevens, Tim J.
Vranken, Wim F.
Vriend, Gert
Vuister, Geerten W.
CING: an integrated residue-based structure validation program suite
title CING: an integrated residue-based structure validation program suite
title_full CING: an integrated residue-based structure validation program suite
title_fullStr CING: an integrated residue-based structure validation program suite
title_full_unstemmed CING: an integrated residue-based structure validation program suite
title_short CING: an integrated residue-based structure validation program suite
title_sort cing: an integrated residue-based structure validation program suite
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3483101/
https://www.ncbi.nlm.nih.gov/pubmed/22986687
http://dx.doi.org/10.1007/s10858-012-9669-7
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