# Protein Protein docking without restraint definitions **URL:** \ **Category:** HADDOCK\ **Created:** [April 24, 2019, 6:14pm UTC](https://ask.bioexcel.eu/t/protein-protein-docking-without-restraint-definitions/1545 "2019-04-24T18:14:54Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![ajaniharesh](https://avatars.discourse-cdn.com/v4/letter/a/b9e5f3/32.png) [@ajaniharesh](https://ask.bioexcel.eu/u/ajaniharesh)\ **Post date:** [April 24, 2019, 6:14pm UTC](https://ask.bioexcel.eu/t/protein-protein-docking-without-restraint-definitions/1545/1 "2019-04-24T18:14:54Z")
Hi Prof. Bonvin, I have experienced with bound ligand protein-protein docking with restraint definition with 5A active site residue from the ligand. HADDOCK generated almost similar poses as reference. Now, assume if I don’t have information about ligand in the second protein. I don’t know the second protein where exactly bind with the first protein. Blindly, I would like to submit a job. Is it possible to submit a job without defining active and passive residues in HADDOCK interface? If yes then I would like to check do I get similar poses like a reference protein. Looking forward to hear from you. Regards, Haresh Ajani ---
**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:** [April 24, 2019, 6:39pm UTC](https://ask.bioexcel.eu/t/protein-protein-docking-without-restraint-definitions/1545/2 "2019-04-24T18:39:56Z")
Well, that’s not the scenario for which HADDOCK was designed. But there is indeed a way to do it. Two scenarios: 1. You do know the binding site on protein 1 but no info for protein 2: In that case define active residues for protein 1 and define all solvent accessible residues of protein 2 as passive 2. You don’t know anything about both proteins: Use in that case either the random AIRs (expert or guru access required) or the centre-of-mass restraints options. Those can be selected in the distance restraints menu: `Random patches` `Define randomly ambiguous interaction restraints from accessible residues` or `Center of mass restraints` `Define center of mass restraints to enforce contact between the molecules ` In both cases do increase the sampling of models for it0 to 10000 and it1/water to 400. I would also suggest to perform then a more statistical analysis of the contacted residues to try to identify possible binding site. Something similar in described in our protein-ligand tutorial at: > **[HADDOCK small molecule binding site screening](http://www.bonvinlab.org/education/HADDOCK-binding-sites/)** > > A small tutorial on identifying putative binding site for small ligands using HADDOCK ---
**Author:** ![ajaniharesh](https://avatars.discourse-cdn.com/v4/letter/a/b9e5f3/32.png) [@ajaniharesh](https://ask.bioexcel.eu/u/ajaniharesh)\ **Post date:** [April 24, 2019, 7:09pm UTC](https://ask.bioexcel.eu/t/protein-protein-docking-without-restraint-definitions/1545/3 "2019-04-24T19:09:51Z")
Thanks Prof. Bonvin for answer. ---
**Author:** ![KarthikIITG](https://avatars.discourse-cdn.com/v4/letter/k/85f322/32.png) [@KarthikIITG](https://ask.bioexcel.eu/u/KarthikIITG)\ **Post date:** [May 6, 2026, 8:01am UTC](https://ask.bioexcel.eu/t/protein-protein-docking-without-restraint-definitions/1545/4 "2026-05-06T08:01:06Z")
Hi. With reference to this. I have a question. Say one antibody (A) binds to domain 2 of a protein (X) and another antibody (B) binds to domain 4 of the same protein (X). I tried to use controls in my experiment. I used active and passive residues (derived from mutagenesis and structural interface) specific to antibody A and protein X (this is my positive control) docked them. The same thing I used for my antibody B which actually binds to domain 4 of that protein. I wanted to use it as a negative control. But HADDOCK does not seem to clearly differentiate between that? I get -110 HADDOCK score for my positive control and -98 for my negative control. Now I am stuck, if I cannot make a good statement why this is happening and then my test samples also wont be accepted right? Please advice me! ---
**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:** [May 6, 2026, 9:47am UTC](https://ask.bioexcel.eu/t/protein-protein-docking-without-restraint-definitions/1545/5 "2026-05-06T09:47:50Z")
Remember docking scores are not binding affinities. Any docking software will always give you an answer and not tell you: no it does not bind. On one side, the good news is that you negative control has a worse score. You could do the reverse experiment targeting domain 4 ---
**Author:** ![KarthikIITG](https://avatars.discourse-cdn.com/v4/letter/k/85f322/32.png) [@KarthikIITG](https://ask.bioexcel.eu/u/KarthikIITG)\ **Post date:** [May 13, 2026, 6:40am UTC](https://ask.bioexcel.eu/t/protein-protein-docking-without-restraint-definitions/1545/6 "2026-05-13T06:40:37Z")
Thank you. So only way to check it, if I run molecular dynamic simulations and see if negative control complex drifts apart while positive control complex stays put? Also. I have submitted few jobs 2 days back (11.05.2026), only 2-3 jobs ran, rest all is still queued. Normally jobs move faster and gets completed in maximum 24 hours. Could you please let me know this will be resolved? ---
**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:** [May 13, 2026, 11:12am UTC](https://ask.bioexcel.eu/t/protein-protein-docking-without-restraint-definitions/1545/7 "2026-05-13T11:12:15Z")
Even MD might not give the answer… Timescales might be too long to see anything… As for the pending runs, there was some grid maintenance yesterday that has caused delays. Be patient. ---
**Author:** ![KarthikIITG](https://avatars.discourse-cdn.com/v4/letter/k/85f322/32.png) [@KarthikIITG](https://ask.bioexcel.eu/u/KarthikIITG)\ **Post date:** [May 13, 2026, 11:56am UTC](https://ask.bioexcel.eu/t/protein-protein-docking-without-restraint-definitions/1545/8 "2026-05-13T11:56:41Z")
Thank you for your prompt response. But if docking + MD (anything below 1 microsecond) cannot distinguish negative and a positive control? Whats the next step to prove that? Will MM-PBSA can show decreased binding affinities significantly for negative control? ---
**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:** [May 14, 2026, 8:17am UTC](https://ask.bioexcel.eu/t/protein-protein-docking-without-restraint-definitions/1545/9 "2026-05-14T08:17:12Z")
What ever computational validation you do, it will remain a prediction…