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Structure calculation, refinement and validation using CcpNmr Analysis
CcpNmr Analysis provides a streamlined pipeline for both NMR chemical shift assignment and structure determination of biological macromolecules. In addition, it encompasses tools to analyse the many additional experiments that make NMR such a pivotal technique for research into complex biological qu...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4304695/ https://www.ncbi.nlm.nih.gov/pubmed/25615869 http://dx.doi.org/10.1107/S1399004714026662 |
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author | Skinner, Simon P. Goult, Benjamin T. Fogh, Rasmus H. Boucher, Wayne Stevens, Tim J. Laue, Ernest D. Vuister, Geerten W. |
author_facet | Skinner, Simon P. Goult, Benjamin T. Fogh, Rasmus H. Boucher, Wayne Stevens, Tim J. Laue, Ernest D. Vuister, Geerten W. |
author_sort | Skinner, Simon P. |
collection | PubMed |
description | CcpNmr Analysis provides a streamlined pipeline for both NMR chemical shift assignment and structure determination of biological macromolecules. In addition, it encompasses tools to analyse the many additional experiments that make NMR such a pivotal technique for research into complex biological questions. This report describes how CcpNmr Analysis can seamlessly link together all of the tasks in the NMR structure-determination process. It details each of the stages from generating NMR restraints [distance, dihedral, hydrogen bonds and residual dipolar couplings (RDCs)], exporting these to and subsequently re-importing them from structure-calculation software (such as the programs CYANA or ARIA) and analysing and validating the results obtained from the structure calculation to, ultimately, the streamlined deposition of the completed assignments and the refined ensemble of structures into the PDBe repository. Until recently, such solution-structure determination by NMR has been quite a laborious task, requiring multiple stages and programs. However, with the new enhancements to CcpNmr Analysis described here, this process is now much more intuitive and efficient and less error-prone. |
format | Online Article Text |
id | pubmed-4304695 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-43046952015-01-30 Structure calculation, refinement and validation using CcpNmr Analysis Skinner, Simon P. Goult, Benjamin T. Fogh, Rasmus H. Boucher, Wayne Stevens, Tim J. Laue, Ernest D. Vuister, Geerten W. Acta Crystallogr D Biol Crystallogr Dynamics CcpNmr Analysis provides a streamlined pipeline for both NMR chemical shift assignment and structure determination of biological macromolecules. In addition, it encompasses tools to analyse the many additional experiments that make NMR such a pivotal technique for research into complex biological questions. This report describes how CcpNmr Analysis can seamlessly link together all of the tasks in the NMR structure-determination process. It details each of the stages from generating NMR restraints [distance, dihedral, hydrogen bonds and residual dipolar couplings (RDCs)], exporting these to and subsequently re-importing them from structure-calculation software (such as the programs CYANA or ARIA) and analysing and validating the results obtained from the structure calculation to, ultimately, the streamlined deposition of the completed assignments and the refined ensemble of structures into the PDBe repository. Until recently, such solution-structure determination by NMR has been quite a laborious task, requiring multiple stages and programs. However, with the new enhancements to CcpNmr Analysis described here, this process is now much more intuitive and efficient and less error-prone. International Union of Crystallography 2015-01-01 /pmc/articles/PMC4304695/ /pubmed/25615869 http://dx.doi.org/10.1107/S1399004714026662 Text en © Skinner et al. 2015 http://creativecommons.org/licenses/by/2.0/uk/ This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited. |
spellingShingle | Dynamics Skinner, Simon P. Goult, Benjamin T. Fogh, Rasmus H. Boucher, Wayne Stevens, Tim J. Laue, Ernest D. Vuister, Geerten W. Structure calculation, refinement and validation using CcpNmr Analysis |
title | Structure calculation, refinement and validation using CcpNmr Analysis
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title_full | Structure calculation, refinement and validation using CcpNmr Analysis
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title_fullStr | Structure calculation, refinement and validation using CcpNmr Analysis
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title_full_unstemmed | Structure calculation, refinement and validation using CcpNmr Analysis
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title_short | Structure calculation, refinement and validation using CcpNmr Analysis
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title_sort | structure calculation, refinement and validation using ccpnmr analysis |
topic | Dynamics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4304695/ https://www.ncbi.nlm.nih.gov/pubmed/25615869 http://dx.doi.org/10.1107/S1399004714026662 |
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