# Investigating the effect of point mutation in the binding affinity of my protein with a ligand **URL:** \ **Category:** Uncategorized\ **Created:** [September 30, 2025, 4:21am UTC](https://ask.bioexcel.eu/t/investigating-the-effect-of-point-mutation-in-the-binding-affinity-of-my-protein-with-a-ligand/5911 "2025-09-30T04:21:20Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![ef25](https://avatars.discourse-cdn.com/v4/letter/e/b38774/32.png) [@ef25](https://ask.bioexcel.eu/u/ef25)\ **Post date:** [September 30, 2025, 4:21am UTC](https://ask.bioexcel.eu/t/investigating-the-effect-of-point-mutation-in-the-binding-affinity-of-my-protein-with-a-ligand/5911/1 "2025-09-30T04:21:20Z")
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/](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. ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [September 30, 2025, 6:10am UTC](https://ask.bioexcel.eu/t/investigating-the-effect-of-point-mutation-in-the-binding-affinity-of-my-protein-with-a-ligand/5911/2 "2025-09-30T06:10:05Z")
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. [ | [CSBPortal](https://rascar.science.uu.nl/haddock2.4/refinement/1) [science.uu.nl](https://rascar.science.uu.nl/haddock2.4/refinement/1) | [![favicon.ico](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/2X/1/107bb531973837ba0aa1bffdc74d58b781de99e8.png)](https://rascar.science.uu.nl/haddock2.4/refinement/1) | ](https://rascar.science.uu.nl/haddock2.4/refinement/1) Remember scores do not represent binding affinity, but they are still informative ---
**Author:** ![ef25](https://avatars.discourse-cdn.com/v4/letter/e/b38774/32.png) [@ef25](https://ask.bioexcel.eu/u/ef25)\ **Post date:** [September 30, 2025, 6:47am UTC](https://ask.bioexcel.eu/t/investigating-the-effect-of-point-mutation-in-the-binding-affinity-of-my-protein-with-a-ligand/5911/3 "2025-09-30T06:47:15Z")
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? ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [September 30, 2025, 7:01am UTC](https://ask.bioexcel.eu/t/investigating-the-effect-of-point-mutation-in-the-binding-affinity-of-my-protein-with-a-ligand/5911/4 "2025-09-30T07:01:03Z")
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) ---
**Author:** ![ef25](https://avatars.discourse-cdn.com/v4/letter/e/b38774/32.png) [@ef25](https://ask.bioexcel.eu/u/ef25)\ **Post date:** [September 30, 2025, 7:20am UTC](https://ask.bioexcel.eu/t/investigating-the-effect-of-point-mutation-in-the-binding-affinity-of-my-protein-with-a-ligand/5911/5 "2025-09-30T07:20:03Z")
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? ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [September 30, 2025, 1:25pm UTC](https://ask.bioexcel.eu/t/investigating-the-effect-of-point-mutation-in-the-binding-affinity-of-my-protein-with-a-ligand/5911/6 "2025-09-30T13:25:17Z")
Send it to bonvinlab.support\_AT\_uu.nl ---
**Author:** ![ef25](https://avatars.discourse-cdn.com/v4/letter/e/b38774/32.png) [@ef25](https://ask.bioexcel.eu/u/ef25)\ **Post date:** [October 3, 2025, 3:34am UTC](https://ask.bioexcel.eu/t/investigating-the-effect-of-point-mutation-in-the-binding-affinity-of-my-protein-with-a-ligand/5911/7 "2025-10-03T03:34:12Z")
Hello! I just want to update that fixed my pdb file already. Thank you for your response here!