Ligand docking and binding site analysis with pymol and autodock/vina

Abstract

Docking of various therapeutically important chemical entities to the specific target sites offers a meaningful strategy that may have tremendous scope in a drug design process. For a thorough understanding of the structural features that determine the strength of bonding between a ligand with its receptor, an insight to visualize binding geometries and interaction is mandatory. Bioinformatical as well as graphical software 'PyMOL' in combination with the molecular docking suites Autodock and Vina allows the study of molecular combination to visualize and understand the structurebased drug design efforts. In the present study, we outlined a user friendly method to perform molecular docking using vina and finally the results were analyzed in pymol in both two as well as three-dimensional orientation. The operation bypasses the steps that are involved in docking using cygwin terminal like formation of gpf and dpf files. The simple and straight-forward operation method does not require formal bioinformatics training to apprehend molecular docking studies using AutoDock 4.2 program.

Molecular docking and simulation studies of natural compounds ofVitex negundoL. against papain-like protease (PLpro) of SARS CoV-2 (coronavirus) to conquer the pandemic situation in the world

“…The molecular binding affinity of the protein ligand complex was predicted using molecular docking analysis. The protocol of docking described by Rauf et al (2015) was used for molecular docking process. A grid box (À39 Å Â 9.8 Å Â 20 Å) centered at (102,98,94) for the PL pro protein of SARS-CoV-2 was used as search space in the docking experiments by utilizing the AutoDock tools.…”

Molecular Docking of Isolated Alkaloids for Possible α-Glucosidase Inhibition

“…Molecular docking is frequently used to predict the binding orientation of small molecules and drug candidates to their protein targets in order to predict their affinity and activity [28,29]. In this study, we modeled various alkaloids isolated from different plants and known for their inhibition of α-glucosidase through molecular docking.…”

Genome-wide analysis of Indian SARS-CoV-2 genomes to identify T-cell and B-cell epitopes from conserved regions based on immunogenicity and antigenicity

“…Moreover, to validate the identified epitopes, the conformational 2D non-covalent structures of the identified epitopes are studied using LigPlot+ [41] . Furthermore, BepiPred2.0 server 10 [42] is used for the verification of the predicted B-cell epitopes.Also, the physico-chemical properties of the epitopes along with Ramachandran plot are reported through PyMOL [43] and its extensive libraries Autodock Vina (for docking) [44] and PyMOD 3 [45] while for the Z-score calculation ProSA 11 [46] online server is used. where, R CCnR represents rank of consensus conserved region (CCnR) based on geometric mean of immunogenic and antigenic scores of T-cell and B-cell epitopes, IS i and AS i are the scaled immunogenic and antigenic scores for MHC-I, MHC-II and B-cell epitopes respectively.…”