# Request for Guidance on Analyzing Protein-Protein Docking Results **URL:** \ **Category:** HADDOCK\ **Created:** [July 9, 2024, 10:05am UTC](https://ask.bioexcel.eu/t/request-for-guidance-on-analyzing-protein-protein-docking-results/5184 "2024-07-09T10:05:19Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![zhuyaojun](https://avatars.discourse-cdn.com/v4/letter/z/f9ae1b/32.png) [@zhuyaojun](https://ask.bioexcel.eu/u/zhuyaojun)\ **Post date:** [July 9, 2024, 10:05am UTC](https://ask.bioexcel.eu/t/request-for-guidance-on-analyzing-protein-protein-docking-results/5184/1 "2024-07-09T10:05:19Z")
Dear HADDOCK Team, I hope this message finds you well. I have performed docking simulations between proteins A and B, as well as between proteins A and C using the HADDOCK tool. From these simulations, I have obtained the following scoring metrics: HADDOCK score Cluster size RMSD from the overall lowest-energy structure Van der Waals energy Electrostatic energy Desolvation energy Restraints violation energy Buried Surface Area Z-Score However, I am uncertain about how to comprehensively analyze these metrics to determine whether the docking between A and B is better or worse compared to the docking between A and C. Therefore, I am seeking your expertise on how to scientifically and effectively compare these docking results based on the provided scoring metrics. Thank you very much for your assistance. Best regards, ---
**Author:** ![zhuyaojun](https://avatars.discourse-cdn.com/v4/letter/z/f9ae1b/32.png) [@zhuyaojun](https://ask.bioexcel.eu/u/zhuyaojun)\ **Post date:** [July 9, 2024, 10:08am UTC](https://ask.bioexcel.eu/t/request-for-guidance-on-analyzing-protein-protein-docking-results/5184/2 "2024-07-09T10:08:05Z")
![屏幕截图 2024-07-09 180617](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/2X/4/494aad8c20fb11197190ff188621eac157fa6e7c.png) ---
**Author:** ![marco.giulini](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/marco.giulini/32/961_2.png) [@marco.giulini](https://ask.bioexcel.eu/u/marco.giulini)\ **Post date:** [July 9, 2024, 10:21am UTC](https://ask.bioexcel.eu/t/request-for-guidance-on-analyzing-protein-protein-docking-results/5184/3 "2024-07-09T10:21:02Z")
Hi, The HADDOCK score should not be used to compare different complexes, but rather to inspect the results obtained within each run. Similar systems might be compared, but I don’t know how similar proteins B and C are in your case. Have a look at this other thread [Problem with interpretation HADDOCK scores](https://ask.bioexcel.eu/t/problem-with-interpretation-haddock-scores/5038) PS: I notice you have a very high restraint energy, maybe check your restraints and/or remove the 10% of that value from the overall HADDOCK score Cheers ---
**Author:** ![zhuyaojun](https://avatars.discourse-cdn.com/v4/letter/z/f9ae1b/32.png) [@zhuyaojun](https://ask.bioexcel.eu/u/zhuyaojun)\ **Post date:** [July 10, 2024, 6:39am UTC](https://ask.bioexcel.eu/t/request-for-guidance-on-analyzing-protein-protein-docking-results/5184/4 "2024-07-10T06:39:34Z")
Thank you ☕ ---
**Author:** ![zhuyaojun](https://avatars.discourse-cdn.com/v4/letter/z/f9ae1b/32.png) [@zhuyaojun](https://ask.bioexcel.eu/u/zhuyaojun)\ **Post date:** [July 10, 2024, 6:42am UTC](https://ask.bioexcel.eu/t/request-for-guidance-on-analyzing-protein-protein-docking-results/5184/5 "2024-07-10T06:42:41Z")
I have connected A-B(TLR2) and A-C(TLR4). However, I can only perform kinetic simulations on one of these complexes, and I am struggling to find a reason to choose between them. Do you have any suggestions? Thank you. ---
**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:** [July 10, 2024, 7:00am UTC](https://ask.bioexcel.eu/t/request-for-guidance-on-analyzing-protein-protein-docking-results/5184/6 "2024-07-10T07:00:40Z")
May-be some MD simulations first could help. Check for example: - Z. Jandova, A.V. Vargiu and A.M.J.J. Bonvin. [Native or non-native protein-protein docking models? Molecular dynamics to the rescue](https://doi.org/10.1021/acs.jctc.1c00336). _J. Chem. Theo. and Comp._ _17_, 5944−5954 (2021). Not really meant to compare different complexes though but rather different clusters of the same complex. ---
**Author:** ![karenf](https://avatars.discourse-cdn.com/v4/letter/k/b5ac83/32.png) [@karenf](https://ask.bioexcel.eu/u/karenf)\ **Post date:** [December 4, 2024, 1:27pm UTC](https://ask.bioexcel.eu/t/request-for-guidance-on-analyzing-protein-protein-docking-results/5184/7 "2024-12-04T13:27:15Z")
If I am docking the same 2 proteins with different ligands, can I compare between them? ---
**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:** [December 4, 2024, 1:55pm UTC](https://ask.bioexcel.eu/t/request-for-guidance-on-analyzing-protein-protein-docking-results/5184/8 "2024-12-04T13:55:49Z")
That would be a better case indeed for comparison. But again, remember that the score is not equal to binding affinity.