AutoDock Tools v1.5.6
AutoDock Tools v1.5.6 is a molecular docking software package that allows users to predict the binding of small molecules to protein targets. The software provides a graphical user interface for preparing input files, running docking calculations, and analyzing the results.
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67 protocols using AutoDock Tools v1.5.6
Molecular Docking of Emodin with SARS-CoV-2 Targets
Acetylcholinesterase Binding Mode Analysis
Protein Preparation and Binding Site Analysis
In silico Screening of Bioactive Compounds
The binding affinity and interactions of the isolated compounds in S. trifasciata were determined using AutoDock. The native ligands (TLM and 629) were redocked to the β-ketoacyl-ACP synthase and TyrRS, respectively, to validate the docking parameters. The validated procedures were identified with a root mean square deviation (RMSD) below 2 Å [40 (link)]. The binding site of β-ketoacyl-ACP synthase and TyrRS were set according to their native ligand positions and calculated using a cubic shape with a grid area of 40 × 40 × 40 Å. The proteins’ and ligands’ hydrogen bonding and hydrophobic interactions were analyzed and visualized employing Discovery Studio Visualizer v.17.2.0.16349 software.
Structural Insights: SEMA3C-RAGE Interactions
Molecular Docking of Compound 5
Structural Receptor Extraction and Molecular Docking
Molecular Docking of Novel TOP1 Inhibitors
AutoDock Vina software [91 (link)] was used to perform docking experiments between the selected compound and TOP1/DNA duplex. A grid box with size 10 × 10 × 10 and centered at X = 94.906 Y = 95.914 Z = 32.500 was used as search space. AutoDock Vina provided the best binding affinity rank for each ligand.
Molecular Docking and QM/MM Optimization of Natural Product Inhibitors Against SARS-CoV-2 Proteases
Small Molecule Structure Optimization
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