AutoDock Vina Tutorial: Molecular Docking for Beginners
Автор: Axonist
Загружено: 2023-07-14
Просмотров: 45599
In this tutorial, we provide a comprehensive step-by-step guide on how to use AutoDock Vina, a powerful software tool for molecular docking and virtual screening in drug discovery. Whether you're a beginner or an experienced researcher, this video will walk you through the entire process of predicting ligand-receptor binding modes and affinities using AutoDock Vina.
The config.txt file must be created manually to define parameters for docking. Here’s how:
Open a text editor and include the following lines (adjust as needed):
receptor = receptor.pdbqt
ligand = ligand.pdbqt
center_x = [X coordinate]
center_y = [Y coordinate]
center_z = [Z coordinate]
size_x = [Size along X-axis]
size_y = [Size along Y-axis]
size_z = [Size along Z-axis]
out = output.pdbqt
exhaustiveness = 8
Adjust for more thorough docking (default is 8)
Replace filenames and coordinates based on your receptor/ligand and the binding site.
Save the file as config.txt in the same directory as your docking files.
Download Tools
MGLTools
https://ccsb.scripps.edu/mgltools/dow...
AutoDock Vina
https://vina.scripps.edu/downloads/
UCSF Chimera
https://www.cgl.ucsf.edu/chimera/down...
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