Hello there,
I have been trying to dock a protein and four peptides (30-32 amino acids) together. I have selected a total of five molecules in HADDOCK 2.4. I am using the default parameters. But when I repeated the docking with the same default parameters, I got different binding sites and different binding energies. Also, they are different the third time. Am I missing something? Can you help me out why this is happening? Which structure can I rely on?