Hello! I have already run the docking of my WT protein with a ligand using haddock (with both distance and dihedral restraints). Now, I am looking into mutating my protein to increase the binding affinity with the ligand. I have already run https://biosig.lab.uq.edu.au/dynamut2/ for looking into the stability of my protein once point mutations are introduced. Is there any software I can look into to generate binding affinities, structural changes, etc of a point mutated protein once it binds to the ligand? I already ahve information on the specific residues in my protein that interacts with the liogand via NMR results. Thank you for your help.
You could try to introduce the mutations in your PDB file (simply changing the residue name - don’t bother about adding/deleting atoms), and use the refinement interface of the HADDOCK server. Also run the WT through the refinement server and compare the scores.
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Remember scores do not represent binding affinity, but they are still informative
Thank you for your suggestion. However, when I try to submit a job in the refinement interface and click “next”, the website just refreshes and not load the job. Are there fixes I can do?
Make sure the ligand in your PDB file is defined as HETATM and has a different chainID than your protein.
If the problem persist, do share your PDB (e.g. via direct email)
It still just refreshes when I click “Next” and then not load the job. I try different PDBs, like the different best structures from my docking run as well as a PDB file from literature. Can I send you my file? May I ask for your email?
Send it to bonvinlab.support_AT_uu.nl
Hello! I just want to update that fixed my pdb file already. Thank you for your response here!