On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge

In the context of the recent SAMPL6 SAMPLing challenge (Rizzi et al. 2020 in J Comput Aided Mol Des 34:601–633) aimed at assessing convergence properties and reproducibility of molecular dynamics binding free energy methodologies, we propose a simple explanation of the severe errors observed in the...

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Autores principales: Procacci, Piero, Macchiagodena, Marina
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2021
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8523005/
https://www.ncbi.nlm.nih.gov/pubmed/34625885
http://dx.doi.org/10.1007/s10822-021-00419-0
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author Procacci, Piero
Macchiagodena, Marina
author_facet Procacci, Piero
Macchiagodena, Marina
author_sort Procacci, Piero
collection PubMed
description In the context of the recent SAMPL6 SAMPLing challenge (Rizzi et al. 2020 in J Comput Aided Mol Des 34:601–633) aimed at assessing convergence properties and reproducibility of molecular dynamics binding free energy methodologies, we propose a simple explanation of the severe errors observed in the nonequilibrium switch double-system-single-box (NS-DSSB) approach when using unidirectional estimates. At the same time, we suggest a straightforward and minimal modification of the NS-DSSB protocol for obtaining reliable unidirectional estimates for the process where the ligand is decoupled in the bound state and recoupled in the bulk. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10822-021-00419-0.
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spelling pubmed-85230052021-10-22 On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge Procacci, Piero Macchiagodena, Marina J Comput Aided Mol Des Article In the context of the recent SAMPL6 SAMPLing challenge (Rizzi et al. 2020 in J Comput Aided Mol Des 34:601–633) aimed at assessing convergence properties and reproducibility of molecular dynamics binding free energy methodologies, we propose a simple explanation of the severe errors observed in the nonequilibrium switch double-system-single-box (NS-DSSB) approach when using unidirectional estimates. At the same time, we suggest a straightforward and minimal modification of the NS-DSSB protocol for obtaining reliable unidirectional estimates for the process where the ligand is decoupled in the bound state and recoupled in the bulk. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10822-021-00419-0. Springer International Publishing 2021-10-09 2021 /pmc/articles/PMC8523005/ /pubmed/34625885 http://dx.doi.org/10.1007/s10822-021-00419-0 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Procacci, Piero
Macchiagodena, Marina
On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge
title On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge
title_full On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge
title_fullStr On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge
title_full_unstemmed On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge
title_short On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge
title_sort on the ns-dssb unidirectional estimates in the sampl6 sampling challenge
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8523005/
https://www.ncbi.nlm.nih.gov/pubmed/34625885
http://dx.doi.org/10.1007/s10822-021-00419-0
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