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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2019
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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. |
format | Online Article Text |
id | pubmed-7515419 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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