Receptor Preparation for Docking - English

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AutoDock4 Tutorials - English

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Autodock
In assessment of receptor preparation for docking , Protein 1DWD has 3 chains. which residue has to be removed Please help. What is the criteria to delete the residue
06-07M 0-10S monikakamboj

Answer last updated on: Aug. 12, 2024, 12:17 p.m.
All hydrogens or only non-polar hydrogen?
Could you please tell me, in the YouTube tutorials on using AutoDock4 in the protein preparation step, they recommend adding all the hydrogen first, then combining the non-polar hydrogen. In what situations do we leave all added hydrogen in the system and when do we use only polar hydrogen?
03-04M 10-20S Ivajull

Answer last updated on: Aug. 9, 2024, 3:54 p.m.

Outline:

Open the ADT GUI. Open the receptor pdb file on the ADT display panel. Delete the water molecules from the receptor structure. Add hydrogens to the receptor structure. Remove the ligand molecule crystallized along with the receptor. Save the current session.