Question: Is there any database to find the protein interfaces that already found experimentally?
0
gravatar for m.koohi.m
2.6 years ago by
m.koohi.m90
United States
m.koohi.m90 wrote:

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?

protein database • 924 views
ADD COMMENTlink modified 2.6 years ago by Khader Shameer17k • written 2.6 years ago by m.koohi.m90
1

Have you tried The Eukaryotic Linear Motif database (http://elm.eu.org) [Dinkel et al., Nucleic Acids Res, 2016]?

ADD REPLYlink written 2.6 years ago by a.zielezinski8.5k

Thank you, these proteins are human proteins. I edited the question.

ADD REPLYlink written 2.6 years ago by m.koohi.m90
3
gravatar for Khader Shameer
2.6 years ago by
Manhattan, NY
Khader Shameer17k wrote:

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

List of interactions https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetIface.pl?pdb=11ba&chain1=A&chain2=B

You can easilty parse the URL and combine using a curl, wget or other libraries to compile a dataset of interface residues.

ADD COMMENTlink written 2.6 years ago by Khader Shameer17k

Thanks for your reply, That was really helpful.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by m.koohi.m90
2
gravatar for natasha.sernova
2.6 years ago by
natasha.sernova3.3k
natasha.sernova3.3k wrote:

See this post:

Important Residues For Protein-Protein Binding

and there Nir link gives protein interface databases:

http://rosettadesigngroup.com/blog/58/10-protein-protein-interface-prediction-servers/

and this article:

Progress and challenges in predicting protein interfaces

http://bib.oxfordjournals.org/content/17/1/117.full

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by natasha.sernova3.3k

Thank you, I edited the question. I don't want to predict them, I just want to find if there is any finding about them experimentally.

ADD REPLYlink written 2.6 years ago by m.koohi.m90
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