Generating All Interacting Partners Of A Protein

Question

[Reyhaneh]

I have a protein A (with a known PDB Code) and I would like to generate all the known proteins which interact with A. The interacting partners of A, can be either known through a 3D complex or through literature. (i do not require the complex structure of A and its partners)

Is there a tool that as input accepts the PDB Code of protein A, and as output gives a list of PDB Codes of the interacting partners of A?

Thanks for the help in advance;

Answer 1

[Giovanni M Dall'Olio]

Note that pdb codes refer to cristal structures and not to proteins. For example, some pdb files contain more than one protein. Plus, there it may be more than one pdb id for the same protein. So, it's better if you use the Uniprot codes directly, they should be included in the pdb file.

To get all the known interactions for a certain protein, there are many databases:

• STRING
• GeneMania
• Mint

It is important to note that these databases return predictions based on the current annotations, and that they may contain a lot of false positives or negatives. You may want to manually check at least some of the interactions found, and read the literature referred in each prediction. It will take some time, but may save you from working on a wrong network.

[Reyhaneh]

Thanks for this. the problem of manual search is that I will have several proteins and for all of them I need to extract the interacting partners.

[Pierre Lindenbaum]

there is a nice API for STRING

Answer 2

[Khader Shameer]

Protein-protein interaction data compiled in the resources mentioned by Giovanni will be a good start. But the interaction data in those databases are derived using multiple methods that includes experimentally validated interactions and computational approaches (text-mining, database search). Such database also provides interactions based on co-expressions and cellular co-localization. You may refer to their original papers for full list of experimental or computational methods. As you are looking at structural interactants of your protein of interests you may look at subset of experimentally validated interactions.

I would recommend the following databases that utilize structural information to derive protein-protein interaction

• iPfam
• 3DID

For protein-complex based interaction data, you can use:

• CORUM

You have to ID mapping using SIFTS to map all interactions to a common ID space (say interactions in PDB level or in level of conserved protein domain in each structure etc.)

[Mo]

@Khader Shaker do you know any tool for CORUM?

[Khader Shameer]

Data is available for download, check sections under...

• download info all Complexes as flat file
• download info all Complexes as PSIMI
• download info Core Complexes as flat file

You can do complex enrichment from gene-list using Enrichr

[Mo]

@Khader Shameer that seems to be a good one, again do you have any script, or any example that I can use to understand the steps in which I should follow? because downloading the data is one thing, parsing your protein IDs there is something else. In fact, I don't know what I must look for or how to get the structure of the data etc. Thanks

[Mo]

@Khader Shameer this enrichment is using genes but I only have a list of proteins IDs from Uniprot. How can I do it?