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

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.

Design and Pharmacological Characterization of α4β1 Integrin Cyclopeptide Agonists: Computational Investigation of Ligand Determinants for Agonism versus Antagonism

“…The best binding conformations of 3a and 3c are shown in Figure , along with 3b and 3d , for comparison. The interactions have been analyzed with BIOVIA DSV2021 and with PacVIEW tool in PacDOCK web server . For brevity, herein only the most relevant features of the complexes are discussed; all specific stabilizing interactions and alternative views are discussed in Supporting Information.…”

“…The interactions have been analyzed with BIOVIA DSV2021 and with PacVIEW tool in PacDOCK web server. 59 For brevity, herein only the most relevant features of the complexes are discussed; all specific stabilizing interactions and alternative views are discussed in Supporting Information . The calculated poses of 12a , 12c , and 15 (Figures S18–S21), and the detail of RO0505376 (Figure S14) into the binding site of the α 4 β 7 headpiece (PDB 3 V4 V), are shown in Supporting Information .…”

“…The interactions have been analyzed with BIOVIA DSV2021 and with PacVIEW tool in PacDOCK web server. 59 All CPPs appear to occupy the same location into the crevice between the subunits, in proximity of the MIDAS center. With the only exception of 3d, within the binding site the Phu 1 -LDV-isoAsp 5 sequence of all CPPs can be read in a clockwise direction (Figure 8).…”

Synthesis, Biological Activity and Molecular Docking of Chimeric Peptides Targeting Opioid and NOP Receptors

“…The ligands are rendered in thick lines; C is rendered in gray, N in blue and O in red. Figure obtained with PacDOCK web server [ 56 , 57 ].…”

Molecular docking and dynamics simulation analysis of the human FXIIa with compounds from the Mcule database

“…To validate this docking protocol, the non-covalent inhibitor benzamidine was redocked to the plasma β-FXIIa crystal. Then, the Root Mean Square Deviation (RMSD) was calculated by comparing the conformations of the docked and the co-crystalized benzamidine [ 16 ]. Finally, the hits in the docking output were ranked based on their least binding energy and only the top ten compounds were selected for further validation.…”