Interaction Data set

Q:

help of your paper “Redefining Nodes and Edges: Relating 3D Structures to Protein Networks Provides Insight
into their Evolution “. Now I need to get those protein in pfam which are involved in interaction and also the crystal structure of them.
I would be very grateful to you if you send me the link to access the more detail format of SIN v0.9 data.

A:

My understanding from your email is that you would like to know the Pfam IDs
and the corresponding crystal structures (ie, the PDB IDs) for the
interactions involved in the SIN. To do this, you will have to process two
separate datasets together, but this will not be difficult. Here are the
steps:

i) access the raw SIN data (http://networks.gersteinlab.org/structint/) At
this page, click on “composite dataset” under the download column for SIN
v0.9 data. This is a list of open reading frame IDs corresponding to each
interaction (the first and third columns), as well as whether the
interaction is taken from Pfam.
ii) open the text file I’ve attached with this email. Each row contains
several pieces of information, but what you would like to do is find the PDB
IDs (contained in the 2nd column) corresponding to each Ensembl Gene ID (the
first column). This Ensembl Gene ID is taken from (i) above.
I should mention that there are two problems with the procedure outlined
above.
The first is that I noticed it will not provide crystal structures for all
interactions. I’m not sure why this is the case. Secondly, for some
interactions, multiple crystal structures are available, and it is not clear
which structure was used in Pfam. Nitin (CC’ed to this email) may know how
to negotiate with these issues. If you are still having difficulty, please
contact Nitin or I again after further efforts to get the data you need.

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