Hi, I want to find which residues from a protein has an interaction with another protein? These proteins are human proteins and I just want to find those proteins that are already found with experiments. I don't want to predict them. Is there any database to find this?
Computing protein interfaces are routine in protein science and widely accepted by theoretical and experimental biologists alike. I have used data from resources like PDBSum: https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=index.html
Here is a list of interface residues for 11BA https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=11ba&template=interfaces.html&o=RESIDUE&l=1
Pictorial representation: https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/RunDimhtml.pl?pdb=11ba&chains=AB&gif=YES
You can easilty parse the URL and combine using a curl, wget or other libraries to compile a dataset of interface residues.
See this post:
and there Nir link gives protein interface databases:
and this article:
Progress and challenges in predicting protein interfaces