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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-10-01
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| Series: | Molecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1420-3049/27/20/6884 |
| _version_ | 1797470882978856960 |
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| author | Jacopo Carbone Alessia Ghidini Antonio Romano Luca Gentilucci Francesco Musiani |
| author_facet | Jacopo Carbone Alessia Ghidini Antonio Romano Luca Gentilucci Francesco Musiani |
| author_sort | Jacopo Carbone |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-09T19:42:14Z |
| format | Article |
| id | doaj.art-410f4dcebe1a4fcaba9c542a911e0c27 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-09T19:42:14Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-410f4dcebe1a4fcaba9c542a911e0c272023-11-24T01:33:04ZengMDPI AGMolecules1420-30492022-10-012720688410.3390/molecules27206884PacDOCK: A Web Server for Positional Distance-Based and Interaction-Based Analysis of Docking ResultsJacopo Carbone0Alessia Ghidini1Antonio Romano2Luca Gentilucci3Francesco Musiani4Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, ItalyDepartment of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, ItalyWiraki, Via Laurentina 749, 00143 Rome, ItalyDepartment of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, ItalyLaboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna, ItalyMolecular 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.https://www.mdpi.com/1420-3049/27/20/6884web servermolecular dockingatom matchingRMSD calculationprotein–ligand interactionsclustering |
| spellingShingle | Jacopo Carbone Alessia Ghidini Antonio Romano Luca Gentilucci Francesco Musiani PacDOCK: A Web Server for Positional Distance-Based and Interaction-Based Analysis of Docking Results Molecules web server molecular docking atom matching RMSD calculation protein–ligand interactions clustering |
| 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 | web server molecular docking atom matching RMSD calculation protein–ligand interactions clustering |
| url | https://www.mdpi.com/1420-3049/27/20/6884 |
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