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How-to dock a ligand with many torsions

This How-to applies to: Any version.
This How-to is intended for: Any audience.

Two types of special treatment for systems with many torsions are described which may enable the user to get reproducible results when docking molecules with many torsional degrees of freedom.

For AutoDock4 systems with more than 10-12 torsions require special treatment. AutoDock Vina is successful with systems up to about 20 or so torsions. Using AutoDock Vina to dock systems with more torsions may require special treatment, too.

Two approaches to try are:

  • break the molecule to be docked into several pieces, and dock each one separately. Then, look for docked conformations that would be consistent with the entire molecule. This method was used many years ago to dock two proteins using AutoDock.
  • dock a small portion from one end of the molecule. Then, extend the molecule, holding the end rigid in the conformation found in the first step, and allowing the new extension to move. Continue this, adding pieces to extend the molecule until the entire molecule is docked. This method was used successfully for a study of peptides bound to antibodies.
by Ruth Huey last modified 2013-01-15 13:44

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