Enhanced Molecular Dynamics Method to Efficiently Increase the Discrimination Capability of Computational Protein–Protein Docking

[Image: see text] Protein–protein docking typically consists of the generation of putative binding conformations, which are subsequently ranked by fast heuristic scoring functions. The simplicity of these functions allows for computational efficiency but has severe repercussions on their discriminat...

Descripción completa

Detalles Bibliográficos
Autores principales: Scafuri, Nicola, Soler, Miguel A., Spitaleri, Andrea, Rocchia, Walter
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2021
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8582249/
https://www.ncbi.nlm.nih.gov/pubmed/34653335
http://dx.doi.org/10.1021/acs.jctc.1c00789
_version_ 1784596945393680384
author Scafuri, Nicola
Soler, Miguel A.
Spitaleri, Andrea
Rocchia, Walter
author_facet Scafuri, Nicola
Soler, Miguel A.
Spitaleri, Andrea
Rocchia, Walter
author_sort Scafuri, Nicola
collection PubMed
description [Image: see text] Protein–protein docking typically consists of the generation of putative binding conformations, which are subsequently ranked by fast heuristic scoring functions. The simplicity of these functions allows for computational efficiency but has severe repercussions on their discrimination capabilities. In this work, we show the effectiveness of suitable descriptors calculated along short scaled molecular dynamics runs in recognizing the nearest-native bound conformation among a set of putative structures generated by the HADDOCK tool for eight protein–protein systems.
format Online
Article
Text
id pubmed-8582249
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher American Chemical Society
record_format MEDLINE/PubMed
spelling pubmed-85822492021-11-12 Enhanced Molecular Dynamics Method to Efficiently Increase the Discrimination Capability of Computational Protein–Protein Docking Scafuri, Nicola Soler, Miguel A. Spitaleri, Andrea Rocchia, Walter J Chem Theory Comput [Image: see text] Protein–protein docking typically consists of the generation of putative binding conformations, which are subsequently ranked by fast heuristic scoring functions. The simplicity of these functions allows for computational efficiency but has severe repercussions on their discrimination capabilities. In this work, we show the effectiveness of suitable descriptors calculated along short scaled molecular dynamics runs in recognizing the nearest-native bound conformation among a set of putative structures generated by the HADDOCK tool for eight protein–protein systems. American Chemical Society 2021-10-15 2021-11-09 /pmc/articles/PMC8582249/ /pubmed/34653335 http://dx.doi.org/10.1021/acs.jctc.1c00789 Text en © 2021 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Scafuri, Nicola
Soler, Miguel A.
Spitaleri, Andrea
Rocchia, Walter
Enhanced Molecular Dynamics Method to Efficiently Increase the Discrimination Capability of Computational Protein–Protein Docking
title Enhanced Molecular Dynamics Method to Efficiently Increase the Discrimination Capability of Computational Protein–Protein Docking
title_full Enhanced Molecular Dynamics Method to Efficiently Increase the Discrimination Capability of Computational Protein–Protein Docking
title_fullStr Enhanced Molecular Dynamics Method to Efficiently Increase the Discrimination Capability of Computational Protein–Protein Docking
title_full_unstemmed Enhanced Molecular Dynamics Method to Efficiently Increase the Discrimination Capability of Computational Protein–Protein Docking
title_short Enhanced Molecular Dynamics Method to Efficiently Increase the Discrimination Capability of Computational Protein–Protein Docking
title_sort enhanced molecular dynamics method to efficiently increase the discrimination capability of computational protein–protein docking
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8582249/
https://www.ncbi.nlm.nih.gov/pubmed/34653335
http://dx.doi.org/10.1021/acs.jctc.1c00789
work_keys_str_mv AT scafurinicola enhancedmoleculardynamicsmethodtoefficientlyincreasethediscriminationcapabilityofcomputationalproteinproteindocking
AT solermiguela enhancedmoleculardynamicsmethodtoefficientlyincreasethediscriminationcapabilityofcomputationalproteinproteindocking
AT spitaleriandrea enhancedmoleculardynamicsmethodtoefficientlyincreasethediscriminationcapabilityofcomputationalproteinproteindocking
AT rocchiawalter enhancedmoleculardynamicsmethodtoefficientlyincreasethediscriminationcapabilityofcomputationalproteinproteindocking

Ejemplares similares