anton-bushuiev / ppiref Goto Github PK
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Home Page: https://zenodo.org/records/10700674
License: MIT License
Dataset and utilities for working with protein-protein interactions in 3D
Home Page: https://zenodo.org/records/10700674
License: MIT License
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.
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
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?
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