I have a list of pairs of gene symbols who interact (putatively) and would like to assign each pair a score (and record other details) based on the predicted Protein-Protein Interaction (PPI). The existing PPI webservers I've looked at (ClusPro and HADDOCK) require that I use PDB ID's as input. Unfortunately, PDB ID's don't always exist for the gene symbols I'd like to compare. I believe I need either:
- a way to generate PDB files myself (perhaps with a folding program?) and then connect/upload them to a PPI webserver.
- a way to find the most similar sequence that does have a PDB ID and upload it to a PPI webserver.
Am I understanding my problem correctly? Are there resources that can help with 1 or 2?