I want to search the inter-domain communication path of a protein. Except Wordom, is there any other softwares that can do this?
Wordom should be the more natural choice to get protein structure network, especially if you are using a structural ensemble for example generated by MD simulations. Otherwise, you can take a look to this other program published few months ago by the group that originally develop the PSN approach: PSN-ENSEMBLE http://vishgraph.mbu.iisc.ernet.in/PSN-Ensemble/psn_index.html.
Or if you feel like you can try PyInteraph, which was developed by my students and me
http://pubs.acs.org/doi/abs/10.1021/ci400639r but it doesn't use the original PSN approach, it builds the network on the base of intra or inter-molecular interactions…
Perhaps you can try both the approaches.
If you then are interested in different ways to get the paths of communication, I also suggest to read these other two works
http://pubs.rsc.org/en/content/articlelanding/2014/fd/c4fd00024b#!divAbstract (it presents the software MONETA)
and then
http://bioinformatics.oxfordjournals.org/content/29/16/2053.long (it presents the software GSATools).
I hope my comments can be useful, they might be a little bit too MD-oriented so really depend what is the source of your structural information...
Wordom should be the more natural choice to get protein structure network, especially if you are using a structural ensemble for example generated by MD simulations. Otherwise, you can take a look to this other program published few months ago by the group that originally develop the PSN approach: PSN-ENSEMBLE http://vishgraph.mbu.iisc.ernet.in/PSN-Ensemble/psn_index.html.
Or if you feel like you can try PyInteraph, which was developed by my students and me
http://pubs.acs.org/doi/abs/10.1021/ci400639r but it doesn't use the original PSN approach, it builds the network on the base of intra or inter-molecular interactions…
Perhaps you can try both the approaches.
If you then are interested in different ways to get the paths of communication, I also suggest to read these other two works
http://pubs.rsc.org/en/content/articlelanding/2014/fd/c4fd00024b#!divAbstract (it presents the software MONETA)
and then
http://bioinformatics.oxfordjournals.org/content/29/16/2053.long (it presents the software GSATools).
I hope my comments can be useful, they might be a little bit too MD-oriented so really depend what is the source of your structural information...
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