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PacDOCK: A Web Server for Positional Distance-Based and Interaction-Based Analysis of Docking Results

Molecular docking is a key method for structure-based drug design used to predict the conformations assumed by small drug-like ligands when bound to their target. However, the evaluation of molecular docking studies can be hampered by the lack of a free and easy to use platform for the complete anal...

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Detalles Bibliográficos
Autores principales: Carbone, Jacopo, Ghidini, Alessia, Romano, Antonio, Gentilucci, Luca, Musiani, Francesco
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9610523/
https://www.ncbi.nlm.nih.gov/pubmed/36296477
http://dx.doi.org/10.3390/molecules27206884
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author Carbone, Jacopo
Ghidini, Alessia
Romano, Antonio
Gentilucci, Luca
Musiani, Francesco
author_facet Carbone, Jacopo
Ghidini, Alessia
Romano, Antonio
Gentilucci, Luca
Musiani, Francesco
author_sort Carbone, Jacopo
collection PubMed
description Molecular docking is a key method for structure-based drug design used to predict the conformations assumed by small drug-like ligands when bound to their target. However, the evaluation of molecular docking studies can be hampered by the lack of a free and easy to use platform for the complete analysis of results obtained by the principal docking programs. To this aim, we developed PacDOCK, a freely available and user-friendly web server that comprises a collection of tools for positional distance-based and interaction-based analysis of docking results, which can be provided in several file formats. PacDOCK allows a complete analysis of molecular docking results through root mean square deviation (RMSD) calculation, molecular visualization, and cluster analysis of docked poses. The RMSD calculation compares docked structures with a reference structure, also when atoms are randomly labelled, and their conformational and positional differences can be visualised. In addition, it is possible to visualise a ligand into the target binding pocket and investigate the key receptor–ligand interactions. Moreover, PacDOCK enables the clustering of docking results by identifying a restrained number of clusters from many docked poses. We believe that PacDOCK will contribute to facilitating the analysis of docking results to improve the efficiency of computer-aided drug design.
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spelling pubmed-96105232022-10-28 PacDOCK: A Web Server for Positional Distance-Based and Interaction-Based Analysis of Docking Results Carbone, Jacopo Ghidini, Alessia Romano, Antonio Gentilucci, Luca Musiani, Francesco Molecules Article Molecular docking is a key method for structure-based drug design used to predict the conformations assumed by small drug-like ligands when bound to their target. However, the evaluation of molecular docking studies can be hampered by the lack of a free and easy to use platform for the complete analysis of results obtained by the principal docking programs. To this aim, we developed PacDOCK, a freely available and user-friendly web server that comprises a collection of tools for positional distance-based and interaction-based analysis of docking results, which can be provided in several file formats. PacDOCK allows a complete analysis of molecular docking results through root mean square deviation (RMSD) calculation, molecular visualization, and cluster analysis of docked poses. The RMSD calculation compares docked structures with a reference structure, also when atoms are randomly labelled, and their conformational and positional differences can be visualised. In addition, it is possible to visualise a ligand into the target binding pocket and investigate the key receptor–ligand interactions. Moreover, PacDOCK enables the clustering of docking results by identifying a restrained number of clusters from many docked poses. We believe that PacDOCK will contribute to facilitating the analysis of docking results to improve the efficiency of computer-aided drug design. MDPI 2022-10-14 /pmc/articles/PMC9610523/ /pubmed/36296477 http://dx.doi.org/10.3390/molecules27206884 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/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 (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Carbone, Jacopo
Ghidini, Alessia
Romano, Antonio
Gentilucci, Luca
Musiani, Francesco
PacDOCK: A Web Server for Positional Distance-Based and Interaction-Based Analysis of Docking Results
title PacDOCK: A Web Server for Positional Distance-Based and Interaction-Based Analysis of Docking Results
title_full PacDOCK: A Web Server for Positional Distance-Based and Interaction-Based Analysis of Docking Results
title_fullStr PacDOCK: A Web Server for Positional Distance-Based and Interaction-Based Analysis of Docking Results
title_full_unstemmed PacDOCK: A Web Server for Positional Distance-Based and Interaction-Based Analysis of Docking Results
title_short PacDOCK: A Web Server for Positional Distance-Based and Interaction-Based Analysis of Docking Results
title_sort pacdock: a web server for positional distance-based and interaction-based analysis of docking results
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9610523/
https://www.ncbi.nlm.nih.gov/pubmed/36296477
http://dx.doi.org/10.3390/molecules27206884
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