# Several antibody-antigen docking problems **URL:** \ **Category:** HADDOCK\ **Created:** [July 27, 2022, 8:53am UTC](https://ask.bioexcel.eu/t/several-antibody-antigen-docking-problems/3823 "2022-07-27T08:53:33Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![Yolo\_yi](https://avatars.discourse-cdn.com/v4/letter/y/43a26b/32.png) [@Yolo\_yi](https://ask.bioexcel.eu/u/Yolo_yi)\ **Post date:** [July 27, 2022, 8:53am UTC](https://ask.bioexcel.eu/t/several-antibody-antigen-docking-problems/3823/1 "2022-07-27T08:53:34Z")
Hello, I am a rookie in antibody-antigen docking, I would appreciate it if you could give some suggestions; HADDOCK is an excellent job that helps me a lot, and I was troubled by some problems when referring to the manual([HADDOCK2.4 Antibody - Antigen tutorial using PDB-tools webserver – Bonvin Lab](https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-antibody-antigen/)). 1. In the step of " Using ProABC-2 to identify the paratope": when using full length of antibody sequence as input, ProABC-2 offers the Fv domain of heavy chain and light chain separately, which residues should be part of the paratope? Is there a standard for reaching a consensus? 2. There are different ways to prepare the structure for HADDOCK input; Using pdb-tools web server and run.py script from " [haddocking][HADDOCK-antibody-antigen](https://github.com/haddocking/HADDOCK-antibody-antigen)\*\*" in local could get different results: pdb-tools web server and local also get some difference, so I want to know which one to choose. 3. Is there a difference between using the structure of full-length and Fv parts as input for paratope prediction？ Will it affect the docking reslut？ Thank you in advance! ---
**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 29, 2022, 7:35am UTC](https://ask.bioexcel.eu/t/several-antibody-antigen-docking-problems/3823/2 "2022-07-29T07:35:59Z")
Dear Yi > 1. In the step of " Using ProABC-2 to identify the paratope": when using full length of antibody sequence as input, ProABC-2 offers the Fv domain of heavy chain and light chain separately, which residues should be part of the paratope? Is there a standard for reaching a consensus? ProABC should identify the 6 hypervariable loops. Make sure that the residue number match the numbering of your processed PDB file (step 2 below). > 1. There are different ways to prepare the structure for HADDOCK input; Using pdb-tools web server and run.py script from " [haddocking][HADDOCK-antibody-antigen](https://github.com/haddocking/HADDOCK-antibody-antigen)\*\*" in local could get different results: pdb-tools web server and local also get some difference, so I want to know which one to choose. Those tools will not change the coordinates. So in principle both should be fine. What kind of differences are you speaking about. > 1. Is there a difference between using the structure of full-length and Fv parts as input for paratope prediction？ Will it affect the docking reslut？ Waste of CPU resources if using the full length - you target anyway the hypervariable loops. ---
**Author:** ![Yolo\_yi](https://avatars.discourse-cdn.com/v4/letter/y/43a26b/32.png) [@Yolo\_yi](https://ask.bioexcel.eu/u/Yolo_yi)\ **Post date:** [July 29, 2022, 9:35am UTC](https://ask.bioexcel.eu/t/several-antibody-antigen-docking-problems/3823/3 "2022-07-29T09:35:26Z")
Thank you so much for your clear reply. The difference is the length of chain, 3 residues at the end may be lost in my case. But I suspect it might be my problem. I’ll test it again. Another question is “From the results of ProABC-2 we see that the variable domains of both light and heavy chain represent roughly the first 110-120 residues of each chain”. I learned that “At the protein sequence level, the light (25kDa) and heavy (50kDa) chains are comprised of two and four sequence homology regions of ~110 amino acid residues, respectively”, so how should I extract the accurate Fv seq from the full sequence? first 110 or first 120 or case by case? ---
**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 29, 2022, 10:05am UTC](https://ask.bioexcel.eu/t/several-antibody-antigen-docking-problems/3823/4 "2022-07-29T10:05:51Z")
Look at the structures. It should become pretty clear where to cut (at the domain boundaries) ---
**Author:** ![Yolo\_yi](https://avatars.discourse-cdn.com/v4/letter/y/43a26b/32.png) [@Yolo\_yi](https://ask.bioexcel.eu/u/Yolo_yi)\ **Post date:** [July 30, 2022, 3:28am UTC](https://ask.bioexcel.eu/t/several-antibody-antigen-docking-problems/3823/5 "2022-07-30T03:28:10Z")
If the structure is not available, what should I 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:** [July 30, 2022, 7:16pm UTC](https://ask.bioexcel.eu/t/several-antibody-antigen-docking-problems/3823/6 "2022-07-30T19:16:32Z")
How can you model a complex without the structure of the antibody…? Haddock does require an input 3D model ---
**Author:** ![Yolo\_yi](https://avatars.discourse-cdn.com/v4/letter/y/43a26b/32.png) [@Yolo\_yi](https://ask.bioexcel.eu/u/Yolo_yi)\ **Post date:** [July 31, 2022, 9:56am UTC](https://ask.bioexcel.eu/t/several-antibody-antigen-docking-problems/3823/7 "2022-07-31T09:56:14Z")
There is a situation in which the structure is not available, so I need to model it. The method of simulating structure is limited to the Fv domain. I have learned that there do have methods to extract the Fv seq from the full-length sequence. Thank you all the same. ---
**Author:** ![Yolo\_yi](https://avatars.discourse-cdn.com/v4/letter/y/43a26b/32.png) [@Yolo\_yi](https://ask.bioexcel.eu/u/Yolo_yi)\ **Post date:** [August 2, 2022, 7:51am UTC](https://ask.bioexcel.eu/t/several-antibody-antigen-docking-problems/3823/8 "2022-08-02T07:51:15Z")
Hello, it’s me again. 😁 1. As we mentioned in the email, we calculate all contacts within a given cutoff to determine the contact residues, so what is the empirical cutoff generally speaking? 9Å is a loose definition? which cutoff is solid? 2. There are the results from contact-chainID, does each column represent “residues num in first chain/chain id/atom/residues number in the second chain/chain id/atom/distance(Å)”? The question is the length of my chain A is 115 amino acids. If not, how should I get the position of the residues in the interaction surface from a PDB file so that I can use them as active residues? Could you give me any suggestions? ```auto 18 A N 33 B N 28.035966 18 A N 33 B CA 27.980521 18 A N 33 B C 26.735026 18 A N 33 B O 25.950225 18 A N 33 B CB 28.123526 18 A CA 33 B N 26.776857 18 A CA 33 B CA 26.745557 ... 132 A CB 146 B N 48.483703 132 A CB 146 B CA 49.626985 132 A CB 146 B C 50.998842 132 A CB 146 B O 51.154802 132 A CB 146 B CB 49.664195 ``` Thank you so much! ---
**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:** [August 2, 2022, 8:07am UTC](https://ask.bioexcel.eu/t/several-antibody-antigen-docking-problems/3823/9 "2022-08-02T08:07:30Z")
Often a 3.9A cutoff is used to detect contacts between heavy atoms. (e.g. this is what is used in LIGPLOT/DIMPLOT). In CAPRI the fraction of native contacts is calculated using a 5A cutoff (heavy atoms) ---
**Author:** ![Yolo\_yi](https://avatars.discourse-cdn.com/v4/letter/y/43a26b/32.png) [@Yolo\_yi](https://ask.bioexcel.eu/u/Yolo_yi)\ **Post date:** [August 3, 2022, 7:34am UTC](https://ask.bioexcel.eu/t/several-antibody-antigen-docking-problems/3823/10 "2022-08-03T07:34:53Z")
Got it; Thank you.