PRODIGY server takes as input the three-dimensional structure of the protein-protein complex in [PDB]or mmCIF format. I would like to calculate binding affinities between virus protein and de novo synthesis peptides (10-14 amino acids). There are three categories, PRODIGY, PRODIGY-LIGAND and PRODIGY-CRYSTAL. May I know which category I should use? May I know what should I put in the structure and interactor 1&2? Structure (Protein only) or Protein-peptide complex?
As protocol itself, for protein-peptide you should use PRODIGY. However, our predictor has not been trained and validated for this kind of interactions. The contribution of the single terms (i.e., number of contacts between charged/polar/apolar residues) has been optimize for protein-protein complexes, and it might differ in the case of protein-peptide.
For this reason, I would not recommend to use PRODIGY unless you can validate the system (your virus protein with similar peptides) with some experimental data first and see whether you are in a similar scale.
Said so, regarding your second question: in “structure” it goes the protein-peptide complex and in “interactor 1&2” it goes the chain identifiers of the protein and the peptide (which have to be different).
I hope this information help. Let us know if you have further questions.