I have lots of phosphorylation site data, obtained from mass spectrometry, which I manage and explore in R. As you'd expect, R has been very handy for finding patterns for these phospho-sites with respect to their primary sequence and secondary structure predictions. Many bioc packages have been helpful along the way. Now I want to explore for patterns in the 3D structure surrounding these phosphorylation sites. Do phospho-sites correlate well with surface accessibility? Inversely with hydrophobicity? With structural loops? Visual exploration of those sites in 3D renderings of their proteins pdb models seems like a good place to start. In pursuit of that, I have dabbled with PyMol, DeepView, Chimera, VMD, and Cn3D, all of which -- along with other similar tools -- have lots to offer. But so far as I can tell, none have any connection to R. Is there any 3D-molecular-vizualization companion to R, similar in spirit to rggobi or Rgraphviz? Commands like these would be very nice: 1) load (<pdb file="">) 2) select (<list of="" residues="">) 3) colorResiduesByProperty (<accessibility|hydrophobicity|..>) I suspect that the demand for something like this is too small to justify the work -- but if anyone has any advice, I'd love to hear it. Thanks! - Paul

Have you looked into Bio3D in R from Grant et al (Bioinformatics 22, 2695-2696). The project URL is: http://mccammon.ucsd.edu/~bgrant/bio3d/index.html I am not sure if it provides the exact utilities you are looking for but it may be worth to take a look. Best, Thomas On Sat, Jul 26, 2008 at 09:21:26AM -0700, Paul Shannon wrote: > I have lots of phosphorylation site data, obtained from mass > spectrometry, which I manage and explore in R. > As you'd expect, R has been very handy for finding patterns for these > phospho-sites with respect > to their primary sequence and secondary structure predictions. Many > bioc packages have been helpful > along the way. > > Now I want to explore for patterns in the 3D structure surrounding > these phosphorylation sites. > Do phospho-sites correlate well with surface accessibility? Inversely > with > hydrophobicity? With structural loops? Visual exploration of those > sites > in 3D renderings of their proteins pdb models seems like a good place > to start. > > In pursuit of that, I have dabbled with PyMol, DeepView, Chimera, VMD, > and Cn3D, all of which -- along > with other similar tools -- have lots to offer. But so far as I can > tell, none have any connection > to R. > > Is there any 3D-molecular-vizualization companion to R, similar in > spirit to rggobi or Rgraphviz? > Commands like these would be very nice: > > 1) load (<pdb file="">) > 2) select (<list of="" residues="">) > 3) colorResiduesByProperty (<accessibility|hydrophobicity|..>) > > I suspect that the demand for something like this is too small to > justify the > work -- but if anyone has any advice, I'd love to hear it. > > Thanks! > > - Paul > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Thomas Girke Assistant Professor of Bioinformatics Director, IIGB Bioinformatic Facility Center for Plant Cell Biology (CEPCEB) Institute for Integrative Genome Biology (IIGB) Department of Botany and Plant Sciences 1008 Noel T. Keen Hall University of California Riverside, CA 92521 E-mail: thomas.girke at ucr.edu Website: http://faculty.ucr.edu/~tgirke Ph: 951-827-2469 Fax: 951-827-4437