I am working on using the application pepspec to identify possible peptides that would bind to a protein of interest but am running into significant difficulties at the actual peptide generation stage.
After running anchordock with three other homologous proteins in order to generate a good estimate of the anchoring residue, I
use the anchor dock output (pdbs, cst files) as input to the pepspec application. The results that I get make no sense as it just outputs pdbfiles with the correct anchor, but with the other residues not connected to the anchor and spread out around the protein structure.
I've ran the pepspec demo, using the provided inputs and have gotten similar results. I guess my ultimate question is whether anyone else has experienced this? I am new to rosetta and running version 3.4, I have not been able to try this on any earlier versions yet. I have attached pictures of the pepspec output pdbs for further clarification