From: lijo s. <lij...@gm...> - 2008-04-18 12:59:50
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Dear Joe, Thanks, what you explained is exactly right. But I would like to visualize only Hub/ Non-Hub proteins out of the PPI network. How could the tool can discriminate proteins into Hub and Non-Hub? Have you used any computational approach? Lijo On Fri, Apr 18, 2008 at 6:18 PM, Joe Ivanic [Contractor, Foreign National] < ji...@bi...> wrote: > Note that an equivalent e-mail with attachments is awaiting moderator > approval. I include original text only below: > > --- > > I believe the person wishes to view protein-protein interaction (PPI) > networks using Jmol. I have been doing this for quite some time. > > Basically a PPI is just a bunch of proteins (nodes) and interactions > (edges) between them. They can be interpreted as networks. However, to view > them one must come up with a geometry. I have treated PPI networks as sort > of big molecules and then optimized node coordinates for a simple "Energy" > objective function (my background is quantum chemistry). > > Of course, some proteins (nodes) will have more interactions than others, > and the ones that have the most, by far, are called hubs. > > I include a .gpr and script file (which reads in the .gpr) and colors some > hubs red, while leaving the other nodes and edges grey. I have actually made > a movie file from this by rotating by a degree, taking a snapshot, etc. The > file uses Jmol to view the PPI network of E. coli determined from a > particular experiment. > > Joe > > > --- > > Dr. Joe Ivanic - Contractor, Foreign National > Scientist > Biotechnology HPC Software Applications Institute > ATTN: MCMR-TT > Building 363, Miller Drive > Ft. Detrick, MD 21702-5012 > > Voice: (301) 619 1976 > Fax: (301) 619 1983 > > -----Original Message----- > From: jmo...@li... [mailto: > jmo...@li...] On Behalf Of Angel Herraez > Sent: Friday, April 18, 2008 8:34 AM > To: jmo...@li... > Subject: Re: [Jmol-users] Hub and Non-Hub > > Hi lijo > > Could you please explain waht do you mean by "hub" and "hub protein"? > Best if you provide an example file > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't > miss this year's exciting event. There's still time to save $100. > Use priority code J8TL2D2. > > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > ------------------------------------------------------------------------- > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference > Don't miss this year's exciting event. There's still time to save $100. > Use priority code J8TL2D2. > > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Manger Projects, SooryaKiran Bioinformatics, Centre for Bioinformatics, University of Kerala, India. +91 4714060948(off) +91 9446515705(res) |