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?
Look forward to your reply.