Distance restraints

1

Hello，I want to ask a question about the Distance restraints, I know restraints are in CNS format, I want to know how to generate the restraints(TBL file) ,Thanks!

2

By hand :slight_smile:

The restraint format is described in our Nature Protocol paper. See:

http://www.nature.com/nprot/journal/v5/n5/abs/nprot.2010.32.html

Also relevant:

https://www.nature.com/articles/s41596-018-0017-6.epdf?author_access_token=PCOdao9At6UPBnGnXKot19RgN0jAjWel9jnR3ZoTv0OMpdiCTExLiiIVHnJ_GM9iTFHQzhmzv8TQRpN4UoHo_SftIscahWHWSW2Cs2suSVugc9yUnz0hK1botwaQ0W5FoANSwLHc7l2f0LB1mRH94g%3D%3D

Examples are also given is various of our online tutorials.

And I am also describing it in a recent BioExcel webinar about the new features of the 2.4 web server:

https://www.youtube.com/watch?v=9dWdaJ5jBqo
3

Thanks for your help,I also want to ask another question. For the Protein-peptide docking ,how many amino acids should the peptide contain?

4

Conformational flexibility / changes are the challenges when dealing with peptides.
So the shorter you can make you sequence the more change you will have to get some reasonable results.

I would really try to remain below 20 a.a. or even less if possible.

5

OK！Thanks for your answer,it helped me a lot. Then I want to ask you another question,for my protein-peptide docking, the peptide contains 30 aa, so will it be bad to do protein-peptide docking using HADDOCK ?

6

You can always try - but it will be challenging.
It also all depends if you have some knowledge on the conformation of your peptide when bound or not (e.g. is it helical?).

Any software will have a hard time with such a peptide.

7

Hello， I am doing Protein-peptide docking, and as described in protein-peptide docking protocol using the HADDOCK webserver, we can use the build_seq.py script
to generate the starting structures,I want to know how can i get the build_seq.py script and use it.Please help me, thanks very muchpymol_peptide|690x252

8

Should be available as supplementary material. But here is the script. Do change the extension from .pdf too .py since the forum does not allow to upload python files3c_build_seq.pdf (6.8 KB)