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Bayesian-Maximum-Entropy Reweighting of IDP Ensembles Based on NMR Chemical Shifts

Bayesian and Maximum Entropy approaches allow for a statistically sound and systematic fitting of experimental and computational data. Unfortunately, assessing the relative confidence in these two types of data remains difficult as several steps add unknown error. Here we propose the use of a valida...

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Autores principales: Crehuet, Ramon, Buigues, Pedro J., Salvatella, Xavier, Lindorff-Larsen, Kresten
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7515419/
http://dx.doi.org/10.3390/e21090898
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author Crehuet, Ramon
Buigues, Pedro J.
Salvatella, Xavier
Lindorff-Larsen, Kresten
author_facet Crehuet, Ramon
Buigues, Pedro J.
Salvatella, Xavier
Lindorff-Larsen, Kresten
author_sort Crehuet, Ramon
collection PubMed
description Bayesian and Maximum Entropy approaches allow for a statistically sound and systematic fitting of experimental and computational data. Unfortunately, assessing the relative confidence in these two types of data remains difficult as several steps add unknown error. Here we propose the use of a validation-set method to determine the balance, and thus the amount of fitting. We apply the method to synthetic NMR chemical shift data of an intrinsically disordered protein. We show that the method gives consistent results even when other methods to assess the amount of fitting cannot be applied. Finally, we also describe how the errors in the chemical shift predictor can lead to an incorrect fitting and how using secondary chemical shifts could alleviate this problem.
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spelling pubmed-75154192020-11-09 Bayesian-Maximum-Entropy Reweighting of IDP Ensembles Based on NMR Chemical Shifts Crehuet, Ramon Buigues, Pedro J. Salvatella, Xavier Lindorff-Larsen, Kresten Entropy (Basel) Article Bayesian and Maximum Entropy approaches allow for a statistically sound and systematic fitting of experimental and computational data. Unfortunately, assessing the relative confidence in these two types of data remains difficult as several steps add unknown error. Here we propose the use of a validation-set method to determine the balance, and thus the amount of fitting. We apply the method to synthetic NMR chemical shift data of an intrinsically disordered protein. We show that the method gives consistent results even when other methods to assess the amount of fitting cannot be applied. Finally, we also describe how the errors in the chemical shift predictor can lead to an incorrect fitting and how using secondary chemical shifts could alleviate this problem. MDPI 2019-09-17 /pmc/articles/PMC7515419/ http://dx.doi.org/10.3390/e21090898 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Crehuet, Ramon
Buigues, Pedro J.
Salvatella, Xavier
Lindorff-Larsen, Kresten
Bayesian-Maximum-Entropy Reweighting of IDP Ensembles Based on NMR Chemical Shifts
title Bayesian-Maximum-Entropy Reweighting of IDP Ensembles Based on NMR Chemical Shifts
title_full Bayesian-Maximum-Entropy Reweighting of IDP Ensembles Based on NMR Chemical Shifts
title_fullStr Bayesian-Maximum-Entropy Reweighting of IDP Ensembles Based on NMR Chemical Shifts
title_full_unstemmed Bayesian-Maximum-Entropy Reweighting of IDP Ensembles Based on NMR Chemical Shifts
title_short Bayesian-Maximum-Entropy Reweighting of IDP Ensembles Based on NMR Chemical Shifts
title_sort bayesian-maximum-entropy reweighting of idp ensembles based on nmr chemical shifts
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7515419/
http://dx.doi.org/10.3390/e21090898
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