# Peptide-protein
**URL:** https://ask.bioexcel.eu/t/peptide-protein/3832
**Category:** Uncategorized
**Created:** [July 31, 2022, 11:53pm UTC](https://ask.bioexcel.eu/t/peptide-protein/3832 "2022-07-31T23:53:18Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@rizkiamaliaputri0198](https://ask.bioexcel.eu/u/rizkiamaliaputri0198)
#### Post date: [July 31, 2022, 11:53pm UTC](https://ask.bioexcel.eu/t/peptide-protein/3832/1 "2022-07-31T23:53:18Z")
Hello, i want to ask a question about peptide-protein docking.
There is no PDB structure for my peptide because i edited one of the amino acids in the sequences, is it ok if i used uscf chimera to draw the structure? and after i draw the structure of my peptide is there any further step to prepare the peptide before we input it on the haddock server for docking?
Thank you.
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [August 1, 2022, 6:51am UTC](https://ask.bioexcel.eu/t/peptide-protein/3832/2 "2022-08-01T06:51:24Z")
You can also use Pymol to build the peptide in various conformations and give an ensemble of structures as starting point for HADDOCK as described in our protein-peptide docking paper.
Some instructions are available at:
[https://www.bonvinlab.org/education/molmod\_online/simulation/#preparing-the-system](https://www.bonvinlab.org/education/molmod_online/simulation/#preparing-the-system)
And relevant papers:
- C. Geng, S. Narasimhan, J. P.G.L.M. Rodrigues and A.M.J.J. Bonvin. [Information-driven, ensemble flexible peptide docking using HADDOCK](https://doi.org/10.1007/978-1-4939-6798-8_8). _Methods in Molecular Biology: Modeling Peptide-Protein Interactions._ Eds Ora Schueler-Furman and Nir London. Humana Press Inc. _1561_, 109-138 (2017).
- M. Trellet, A.S.J. Melquiond and A.M.J.J. Bonvin. [Information-driven modelling of protein-peptide complexes.](https://link.springer.com/protocol/10.1007/978-1-4939-2285-7_10) _Methods in Molecular Biology._ Ed. Peng Zhou. Humana Press Inc. 221-239 (2015)
- M. Trellet, A.S.J. Melquiond and A.M.J.J. Bonvin. [A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking](https://dx.plos.org/10.1371/journal.pone.0058769) _PLoS ONE_, _8(3)_ e58769 (2013).