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.

Carbone, J., Ghidini, A., Romano, A., Gentilucci, L., Musiani, F. (2022). PacDOCK: A Web Server for Positional Distance-Based and Interaction-Based Analysis of Docking Results. MOLECULES, 27(20), 1-12 [10.3390/molecules27206884].

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

Gentilucci, Luca
;
Musiani, Francesco
Ultimo
2022

Abstract

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.
2022
Carbone, J., Ghidini, A., Romano, A., Gentilucci, L., Musiani, F. (2022). PacDOCK: A Web Server for Positional Distance-Based and Interaction-Based Analysis of Docking Results. MOLECULES, 27(20), 1-12 [10.3390/molecules27206884].
Carbone, Jacopo; Ghidini, Alessia; Romano, Antonio; Gentilucci, Luca; Musiani, Francesco
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11585/899415
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