Hello, recently I began to learn to use HADDOCK for molecular docking, I would like to ask, if I want to a protein and an eight-amino acid peptide chain for molecular docking, then when I submitted the document, what type of molecule should I choose? Should I choose peptide? Then how should the rating function set the weights？
The peptide setting for the peptide.
This will give more flexibility to the peptide.
If you don’t want that, simple define it as protein
Thank you for your answer, and I would also like to ask how the score function should be set up
Simply use the default settings.
Thank you very much for your help！
Hello professor, how are you? I need to dock a 10 amino acid peptide with another protein, is there a requirement for the structure of this peptide, and can I dock it directly with the primary structure?
You will need to provide a starting structure for the peptide.
Check our protein-peptide docking paper on this topic:
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).