# Protein and peptide-dna complex docking **URL:** \ **Category:** HADDOCK\ **Created:** [March 10, 2017, 8:38am UTC](https://ask.bioexcel.eu/t/protein-and-peptide-dna-complex-docking/312 "2017-03-10T08:38:23Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![LIU](https://avatars.discourse-cdn.com/v4/letter/l/a88e57/32.png) [@LIU](https://ask.bioexcel.eu/u/LIU)\ **Post date:** [March 10, 2017, 8:38am UTC](https://ask.bioexcel.eu/t/protein-and-peptide-dna-complex-docking/312/1 "2017-03-10T08:38:23Z")
The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to [http://www.bonvinlab.org/software/haddock2.2](http://www.bonvinlab.org/software/haddock2.2) Dear Alexandre and HADDOCK users, I want to do protein -dna docking by haddock2.2. The situation in my case is : 1. The interaction between my protein A and DNA is weak. The DNA binding sites on protein A can be mapped through NMR titration and the structure of protein A has been solved. But the protein A binding sites on DNA can not be verified. 2. To solve the problem of 1), we found that peptide B can tightly bind with DNA in the minor groove. The structure of peptide B with DNA is known. Then we linked protein A with peptide B and got the protein A- peptide B by expression. But we failed to detect inter-NOES between protein and DNA. My question is how I can do the docking between protein A and the complex of peptide B-DNA by HADDOCK2.2. I know that there is a multi-body docking mode in HADDOCK2.2. But as described above, the protein A and peptide B has been integrated into a whole protein and the peptide B is flexible in solution and no interaction with protein A. The orientation of the protein A should be limited by the existence of peptide B, not like separately docking. In that case, how can I do the docking with the peptide B-DNA complex using protein A? Thanks in advance. Best Changdong ---
**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:** [March 10, 2017, 2:41pm UTC](https://ask.bioexcel.eu/t/protein-and-peptide-dna-complex-docking/312/2 "2017-03-10T14:41:13Z")
> My question is how I can do the docking between protein A and the complex of > peptide B-DNA by HADDOCK2.2. Give the complex of the peptide and DNA to HADDOCK. BUT their residue numbering should not overlap (several threads about this in this forum) and they should have a unique chainID. In the web portal, define it then as protein-DNA for the molecule type And do you have restraints between your protein and the peptide? ---
**Author:** ![LIU](https://avatars.discourse-cdn.com/v4/letter/l/a88e57/32.png) [@LIU](https://ask.bioexcel.eu/u/LIU)\ **Post date:** [March 11, 2017, 5:45am UTC](https://ask.bioexcel.eu/t/protein-and-peptide-dna-complex-docking/312/3 "2017-03-11T05:45:55Z")
Dear Alexandre, Thanks for your reply. There are no any restraints between protein and the peptide. Best Changdong ---
**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:** [March 13, 2017, 8:22am UTC](https://ask.bioexcel.eu/t/protein-and-peptide-dna-complex-docking/312/4 "2017-03-13T08:22:35Z")
So how were you planning to dock the protein onto the peptide-DNA complex? ---
**Author:** ![LIU](https://avatars.discourse-cdn.com/v4/letter/l/a88e57/32.png) [@LIU](https://ask.bioexcel.eu/u/LIU)\ **Post date:** [March 13, 2017, 12:04pm UTC](https://ask.bioexcel.eu/t/protein-and-peptide-dna-complex-docking/312/5 "2017-03-13T12:04:25Z")
Dear Alexandre, There is no interaction between peptide and protein. And peptide and protein are linked by 4 residues, GSGS, as a whole molecule. Can I integrate the protein into peptide-DNA complex and allow the protein to do the docking based on CSP data? Best Changdong ---
**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:** [March 13, 2017, 12:28pm UTC](https://ask.bioexcel.eu/t/protein-and-peptide-dna-complex-docking/312/6 "2017-03-13T12:28:27Z")
So you do have info for docking the protein! (The CSP data). Follow then the protocol in my first answer: - One molecule: the protein - The other molecule: the peptide/DNA complex Define your restraints based on CSP data (are these for the protein side only?) What about the DNA info? Add a loose distance restraint between your protein and the peptide to mimic the GSGS linkage ---
**Author:** ![LIU](https://avatars.discourse-cdn.com/v4/letter/l/a88e57/32.png) [@LIU](https://ask.bioexcel.eu/u/LIU)\ **Post date:** [March 13, 2017, 2:36pm UTC](https://ask.bioexcel.eu/t/protein-and-peptide-dna-complex-docking/312/7 "2017-03-13T14:36:57Z")
Dear Alexandre, Yes, only the CSP data for protein is available and I can not get the CSP data for DNA. Both the peptide and protein recognize the GAAATTC fragment of the 12bp B-form DNA. Based on the structure of the peptide/DNA complex and the biochemical data, the peptide and protein bind the minor and major groove of the GAAATTC fragment respectively, how do I define the restraints for dna? Thanks. Best Changdong ---
**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:** [March 14, 2017, 8:26am UTC](https://ask.bioexcel.eu/t/protein-and-peptide-dna-complex-docking/312/8 "2017-03-14T08:26:25Z")
I would then define as passive in HADDOCK the GAATTC fragment ---
**Author:** ![LIU](https://avatars.discourse-cdn.com/v4/letter/l/a88e57/32.png) [@LIU](https://ask.bioexcel.eu/u/LIU)\ **Post date:** [March 15, 2017, 8:16am UTC](https://ask.bioexcel.eu/t/protein-and-peptide-dna-complex-docking/312/9 "2017-03-15T08:16:44Z")
Dear Alexandre, If define the GAATTC fragment as passive in HADDOCK, how do I define the active sites of the DNA? As the protein binds with the GAATTC fragment, leave the active sites of the DNA blank or the whole dna as active? Best Changdong ---
**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:** [March 15, 2017, 8:31am UTC](https://ask.bioexcel.eu/t/protein-and-peptide-dna-complex-docking/312/10 "2017-03-15T08:31:35Z")
No active on the DNA, only on the protein based on your CSP data