autodock4

AutoDock for GPUs and other accelerators

(Windows) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina

Useful automation and filtering scripts for AutoDock softwares, espacially for large ligand sets.

A script to run docking experiments in AutoDock Vina for several ligands at once with technical replicates.

🔬 Autodock and Vina docking proccess

A bioinformatics project demonstrating molecular docking of phytochemical compounds with the 1VFV protein. The workflow includes protein preparation, ligand preparation, molecular docking, and visualization of protein–ligand interactions using AutoDock4, AutoDockTools, Discovery Studio Visualizer, and AutoDock Vina

Three Nigella sativa alkaloids (indazoles nigellidine, nigellicine; isoquinoline nigellimine) vs S. aureus FtsZ (PDB 3VOA): ADMET screening; docking with Vina, AutoDock4, GNINA, DiffDock-L (redock RMSD 0.307 Å); 4I55 tubulin counter-screen; 100 ns MD; MM-GBSA −13.28 ± 0.97 kcal/mol (SD). Computational predictions only.

VSpipe-GUI: Open-source Python GUI for structure-based virtual screening, molecular docking (AutoDock Vina/AD4), ligand efficiency profiling, and hit selection — published in Int. J. Mol. Sci. (2024)

PyMOL 3.x plugin for visualization of AutoDock4 and AutoDock Vina docking results with interactive Qt controls.

This script automates the molecular docking process using AutoDock. It performs a series of steps to prepare and dock ligands against a protein receptor, handling multiple ligands in the current directory.

Scripts for running and parallelizing AutoDock Vina virtual screening (Linux/Windows/SGE cluster)

Config-driven docking pipeline: AutoDock, Vina, Smina in one workflow