molecular_docking.md

Molecular Docking Protein-Ligand

Software	Video Tutorials
AutoDock Vina	AutoDock Vina
DockingAppRF

Useful literature

• Forli, S., Huey, R., Pique, M. et al. Computational protein–ligand docking and virtual drug screening with the AutoDock suite. Nat Protoc 11, 905–919 (2016). https://doi.org/10.1038/nprot.2016.051

Graphical Interfaces

• PyMOL AutoDock/Vina plugin
• DockingApp

Interaction analysis

• LigPlot
• PLIP

Other Tutorials

• Rizzo Lab

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Molecular Docking Protein-Protein

Software	Tutorials
HDOCK	HDOCK
ClusPro	ClusPro
HADDOCK	HADDOCK

Useful literature

• Yan, Y., Tao, H., He, J. et al. The HDOCK server for integrated protein–protein docking. Nat Protoc 15, 1829–1852 (2020). https://doi.org/10.1038/s41596-020-0312-x
• Kozakov, D., Hall, D., Xia, B. et al. The ClusPro web server for protein–protein docking. Nat Protoc 12, 255–278 (2017). https://doi.org/10.1038/nprot.2016.169