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.
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
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. 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. 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 PLoS ONE, 8(3) e58769 (2013).