Protein protein interactions
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6 weeks ago

Hello all ,

I have the human protein .I need to find its interacting partners that is I need to find that which proteins it is interacting with for regulation and what are the sites within this protein where it interacts with these proteins .If there is any database for such type of information kindly suggest.

Thank you

protein partners interacting interaction • 722 views
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Hi,

STRING

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It only provides the network of proteins interacting with the given protein but what I need is also the residue information that are interacting between the two proteins .

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6 weeks ago
Mensur Dlakic ★ 23k

What you want to do can be be done only on a case-by-case basis, as there is no database that contains information about interacting residues for ALL protein complexes. This is because most protein complexes have not be characterized at that level of detail.

You already have a STRING suggestion, which will tell you the likely interacting partners. From that point on you may have to be content with predicting interacting residues. To do that, there is a website that measures evolutionary couplings:

https://evcouplings.org/

Within that site there are predictions for E. coli complexes, or you can submit proteins of interest to EVcomplex server.

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Sir, How much time does this server take to give output for 1 pair of proteins as I have submitted several hours ago and it still shows running .

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This is not a trivial calculation nor a simple sequence comparison like with BLAST, so it may take a while. Besides, there could be hundreds of users ahead of you in the queue and their jobs will have higher priority than yours.

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Actualy it is showing me the error that that job is running for too long .What can be the possible reasons for this?

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There are all kinds of reasons, starting with an incorrectly formatted input you provided. I think you should contact the authors who maintain the website, as I am not in a position to troubleshoot this for you.

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Thank you Sir