There is a large protein that I would dock a file containing 3 different ligands with to see if distinct binding sites are filled or not. Is any software to do so?
they are seemingly limited to one ligand docking
Thank you in advance
Sargol Mazraedoost
Autodock Vina:Autodock Vina is an extension of the Autodock software and allows for the docking of multiple ligands. You can provide a file containing all ligands, and Vina will attempt to dock each ligand independently. PyRx (Python Prescription):PyRx is a user-friendly interface for Autodock, and it supports multiple ligand docking. It simplifies the process of preparing and running docking experiments. Schrodinger Suite (Glide):Schrodinger's Glide software is widely used for molecular docking. It has the capability to dock multiple ligands to a protein simultaneously. DOCK:DOCK is a molecular docking software that can handle multiple ligands. It is particularly useful for virtual screening of compound libraries against a target protein. RosettaLigand:RosettaLigand, part of the Rosetta suite, supports the docking of multiple ligands. It uses a flexible docking protocol. MOE (Molecular Operating Environment):MOE provides tools for protein-ligand docking, and it supports the docking of multiple ligands to a protein.
Here are a few popular docking tools that allow for multiple-ligand docking:
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Jobin Thomas
You can use AutoDock Vina for the same (freely available).... You can run it on linux system or cmd in windows.... you can refer to tutorials available in youtube..
Regards
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