After the protein structure prediction using AlphaFold2, I want to proceed with molecular docking in Autodock. However, the modelled protein structure cannot be opened using Autodock with the following error. What might be the problem?
Annemarie Honegger
Thank you for the response. Please find the attached file.
Kumari Uma Mahto
I have "cleaned" the pdb file and saved it with the suffix "_R1". Please let me know if the revised file works for you. Thanks.
Rudy J Richardson
Thank you, sir. It works now. Can you please share the procedure to clean these kinds of pdb files.
Kumari Uma Mahto
Thank you for letting me know that the cleaned file worked for you. I am glad.
The procedure I used was to load the file into YASARA-Structure, set the force field to YASARA2, which is a refined version of AMBER14, and execute the "Clean" command, which automatically carries out 39 procedures that I have listed in the attached PDF file.
If you do not have YASARA-Structure, I think there are various free programs or web servers that could accomplish what is needed to enable the file to be used in subsequent docking simulations. Probably the main things are to add hydrogens and ensure that the atom names are consistent with what is required by the docking software.
I am also facing a similar issue during the docking process.
Can anyone help in cleaning these pdb files?
Krishna Palit
It should be possible to prepare your AlphaFold structures for docking using UCSF ChimeraX:
https://www.rbvi.ucsf.edu/chimerax/
This is a free program. It also has special features related to AlphaFold.
However, please note that caveats have been raised regarding the use of AlphaFold structures as docking targets:
Preprint How good are AlphaFold models for docking-based virtual screening?
You can use ReverseDock for your purpose:
https://reversedock.biologie.uni-freiburg.de/
SwissPDB viewer can also be of use. Just open the obtained pdb file in swisspdbview and export and save new file in .pdb format.
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