anton-bushuiev / ppiref Goto Github PK

Hi @anton-bushuiev, nice work and congrats on the ICLR acceptance.

I noticed there are some instances of incorrect interfaces in the raw set e.g. 7lgq_D_H.pdb which only contains a single atom for chain H. Is this intended?

Hello, this is a very good work, but I found a problem that bothered me during use. I used a protein 7qih_A_B (CASP15 name: H1106) to search for similar PPIs and found that only 1xxh_A_B (IDist = 0.0303 IS-score = 0.146) was searched. Further, I used two prediction models of 7qih (completely different docking modes, one of which was a high-scoring prediction model TM: 0.933 and the other was a low-scoring prediction model TM: 0.194) to search for similar PPIs, but got the same result. This is a very strange phenomenon.
High quality model:

PPI search results：

Low quality model:

PPI search results：

Hi @anton-bushuiev,

The zenodo file ppi_6A.zip file does n’t seem to be in ‘.zip’ format. I am unable to extract it.

Also the download.sh file and ppi_extractor.py scripts for PPI extraction does n’t work. The link for pdb rsync is not working for download and many of the threads in ppi_extractor.py gives error after running for sometime.

Would be great if you could fix this.

Regards
Rakesh

Hello.
Thanks for this awesome work.
I am trying to understand if there is a way to search for all PPIs for a query structure/sequence from the complete PPIRef database.
i.e. Suppose I want to find all the interactions made by Lysozyme in any of the available structures. Can I query the PPIRef database for Lysozyme sequence/structure?
I would be really grateful for any insights.
Best,
Amin.