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Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics
Accurate and precise structural ensembles of proteins and macromolecular complexes can be obtained with metainference, a recently proposed Bayesian inference method that integrates experimental information with prior knowledge and deals with all sources of errors in the data as well as with sample h...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4999896/ https://www.ncbi.nlm.nih.gov/pubmed/27561930 http://dx.doi.org/10.1038/srep31232 |
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author | Bonomi, Massimiliano Camilloni, Carlo Vendruscolo, Michele |
author_facet | Bonomi, Massimiliano Camilloni, Carlo Vendruscolo, Michele |
author_sort | Bonomi, Massimiliano |
collection | PubMed |
description | Accurate and precise structural ensembles of proteins and macromolecular complexes can be obtained with metainference, a recently proposed Bayesian inference method that integrates experimental information with prior knowledge and deals with all sources of errors in the data as well as with sample heterogeneity. The study of complex macromolecular systems, however, requires an extensive conformational sampling, which represents a separate challenge. To address such challenge and to exhaustively and efficiently generate structural ensembles we combine metainference with metadynamics and illustrate its application to the calculation of the free energy landscape of the alanine dipeptide. |
format | Online Article Text |
id | pubmed-4999896 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-49998962016-09-07 Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics Bonomi, Massimiliano Camilloni, Carlo Vendruscolo, Michele Sci Rep Article Accurate and precise structural ensembles of proteins and macromolecular complexes can be obtained with metainference, a recently proposed Bayesian inference method that integrates experimental information with prior knowledge and deals with all sources of errors in the data as well as with sample heterogeneity. The study of complex macromolecular systems, however, requires an extensive conformational sampling, which represents a separate challenge. To address such challenge and to exhaustively and efficiently generate structural ensembles we combine metainference with metadynamics and illustrate its application to the calculation of the free energy landscape of the alanine dipeptide. Nature Publishing Group 2016-08-26 /pmc/articles/PMC4999896/ /pubmed/27561930 http://dx.doi.org/10.1038/srep31232 Text en Copyright © 2016, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Bonomi, Massimiliano Camilloni, Carlo Vendruscolo, Michele Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics |
title | Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics |
title_full | Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics |
title_fullStr | Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics |
title_full_unstemmed | Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics |
title_short | Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics |
title_sort | metadynamic metainference: enhanced sampling of the metainference ensemble using metadynamics |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4999896/ https://www.ncbi.nlm.nih.gov/pubmed/27561930 http://dx.doi.org/10.1038/srep31232 |
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