How to predict Protein-Protein Interactions from a pair of gene symbols?

Question

[burkhart.joshua]

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:

1. a way to generate PDB files myself (perhaps with a folding program?) and then connect/upload them to a PPI webserver.

or

1. 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?

Answer 1

[Nestor Wendt]

First, I would try to find an entry at PDB for the genes you have. I suppose you have (or can obtain) the sequences for these genes. Note that one gene can have several isoforms. To do that, a simple blastx or blastp search in the PDB database is enough. That can be done through the NCBI BLAST. Look for exact matches.

After that, for those genes without a suitable PDB model you can try comparative modelling. I suggest either SWISS-MODEL (faster) or I-TASSER. Note that not every sequence may produce a good model. Don't ever blindly trust the results!

Finally, after you have all (or most) PDB models, you can use HADDOCK for PPI. It's quite easy. If HADDOCK does not like your PDB files due to bad formatting this repo has a lot of good scripts that can help.