Re: [IMP-users] How to represent a protein-protein interaction network in IMP

[Daniel Russel <>]

I'd look at one of the general graph libraries (eg networkx in python or boost.graph in c++) for the graph data management and than map things to connectivity restraints as appropriate.Â

   Daniel

On Friday, November 1, 2013, Hongzhu Cui wrote:

Hi, Daniel,

Many Thanks.

We would like to input a network, which means a set of binary proteins with interaction, and hope IMP could produce a graph of the network. Also, we want to represent some biological restraints on the protein-protein interaction we generalized in IMP, reduce some interactions and optimize the network.Â

So, could you give me some more advice?

Thank,again,

Hongzhu

--

Hongzhu Cui, PhD Student

University of Missouri

Informatics Institute

246 Engineering Building West

Columbia, MO 65211

phone: +1(573)239-1592

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2013/11/1 Daniel Russel <');" target="_blank">>

Can you provide a bit more information about what you want to do with the network? Are you looking to find a structure? Or produce a graph of the network at the end?

The connectivity restraints may be something you want to look at core::ConnectivityRestraint and core::MSConnectivityRestraint and atom::create_connectivity_restraint().

On Thu, Oct 31, 2013 at 10:13 PM, Hongzhu Cui <');" target="_blank">> wrote:

Hi, all,Â

Recently, I have a project with IMP. Basically, we need to represent a protein-protein interaction network in IMP, and then we add some restraints to see how we could optimize this network. But I stuck on this problem, and I did not find any similar example in the Manual documentation.

Thanks & Regards,

Hongzhu

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