Hi, all,
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
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 cuihzh@gmail.com wrote:
> > Hi, all, > > 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 > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > >
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.
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 e-mail: cuihzh@gmail.com; hcxk9@mail.missouri.edu
2013/11/1 Daniel Russel drussel@gmail.com
> 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 cuihzh@gmail.com wrote: > >> >> Hi, all, >> >> 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 >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users >> >> > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > >
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.
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. > > 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 > e-mail: cuihzh@gmail.com <javascript:_e({}, 'cvml', 'cuihzh@gmail.com');>; > hcxk9@mail.missouri.edu <javascript:_e({}, 'cvml', > 'hcxk9@mail.missouri.edu');> > > > 2013/11/1 Daniel Russel <drussel@gmail.com <javascript:_e({}, 'cvml', > 'drussel@gmail.com');>> > >> 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 <cuihzh@gmail.com<javascript:_e({}, 'cvml', 'cuihzh@gmail.com');> >> > wrote: >> >>> >>> Hi, all, >>> >>> 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 >>> >>> _______________________________________________ >>> IMP-users mailing list >>> IMP-users@salilab.org <javascript:_e({}, 'cvml', >>> 'IMP-users@salilab.org');> >>> https://salilab.org/mailman/listinfo/imp-users >>> >>> >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org <javascript:_e({}, 'cvml', >> 'IMP-users@salilab.org');> >> https://salilab.org/mailman/listinfo/imp-users >> >> >
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Daniel Russel -
Hongzhu Cui