Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges

We systematically tested the Autodock4 docking program for absolute binding free energy predictions using the host-guest systems from the recent SAMPL6, SAMPL7 and SAMPL8 challenges. We found that Autodock4 behaves surprisingly well, outperforming in many instances expensive molecular dynamics or qu...

Descripción completa

Detalles Bibliográficos
Autores principales: Casbarra, Lorenzo, Procacci, Piero
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2021
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8141411/
https://www.ncbi.nlm.nih.gov/pubmed/34027592
http://dx.doi.org/10.1007/s10822-021-00388-4
_version_ 1783696359640006656
author Casbarra, Lorenzo
Procacci, Piero
author_facet Casbarra, Lorenzo
Procacci, Piero
author_sort Casbarra, Lorenzo
collection PubMed
description We systematically tested the Autodock4 docking program for absolute binding free energy predictions using the host-guest systems from the recent SAMPL6, SAMPL7 and SAMPL8 challenges. We found that Autodock4 behaves surprisingly well, outperforming in many instances expensive molecular dynamics or quantum chemistry techniques, with an extremely favorable benefit-cost ratio. Some interesting features of Autodock4 predictions are revealed, yielding valuable hints on the overall reliability of docking screening campaigns in drug discovery projects. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10822-021-00388-4.
format Online
Article
Text
id pubmed-8141411
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Springer International Publishing
record_format MEDLINE/PubMed
spelling pubmed-81414112021-05-24 Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges Casbarra, Lorenzo Procacci, Piero J Comput Aided Mol Des Article We systematically tested the Autodock4 docking program for absolute binding free energy predictions using the host-guest systems from the recent SAMPL6, SAMPL7 and SAMPL8 challenges. We found that Autodock4 behaves surprisingly well, outperforming in many instances expensive molecular dynamics or quantum chemistry techniques, with an extremely favorable benefit-cost ratio. Some interesting features of Autodock4 predictions are revealed, yielding valuable hints on the overall reliability of docking screening campaigns in drug discovery projects. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10822-021-00388-4. Springer International Publishing 2021-05-24 2021 /pmc/articles/PMC8141411/ /pubmed/34027592 http://dx.doi.org/10.1007/s10822-021-00388-4 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
Casbarra, Lorenzo
Procacci, Piero
Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges
title Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges
title_full Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges
title_fullStr Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges
title_full_unstemmed Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges
title_short Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges
title_sort binding free energy predictions in host-guest systems using autodock4. a retrospective analysis on sampl6, sampl7 and sampl8 challenges
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8141411/
https://www.ncbi.nlm.nih.gov/pubmed/34027592
http://dx.doi.org/10.1007/s10822-021-00388-4
work_keys_str_mv AT casbarralorenzo bindingfreeenergypredictionsinhostguestsystemsusingautodock4aretrospectiveanalysisonsampl6sampl7andsampl8challenges
AT procaccipiero bindingfreeenergypredictionsinhostguestsystemsusingautodock4aretrospectiveanalysisonsampl6sampl7andsampl8challenges

Ejemplares similares