Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Skinner, Simon P., Goult, Benjamin T., Fogh, Rasmus H., Boucher, Wayne, Stevens, Tim J., Laue, Ernest D., Vuister, Geerten W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2015
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
_version_ 1782354145506754560
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
title_full Structure calculation, refinement and validation using CcpNmr Analysis
title_fullStr Structure calculation, refinement and validation using CcpNmr Analysis
title_full_unstemmed Structure calculation, refinement and validation using CcpNmr Analysis
title_short Structure calculation, refinement and validation using CcpNmr Analysis
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
work_keys_str_mv AT skinnersimonp structurecalculationrefinementandvalidationusingccpnmranalysis
AT goultbenjamint structurecalculationrefinementandvalidationusingccpnmranalysis
AT foghrasmush structurecalculationrefinementandvalidationusingccpnmranalysis
AT boucherwayne structurecalculationrefinementandvalidationusingccpnmranalysis
AT stevenstimj structurecalculationrefinementandvalidationusingccpnmranalysis
AT laueernestd structurecalculationrefinementandvalidationusingccpnmranalysis
AT vuistergeertenw structurecalculationrefinementandvalidationusingccpnmranalysis