Dear Alden,Thank you for your reply and your information. My idea is very similar to the idea presented in this nice paper. But the the approaches they used are beyond the limit of my knowledge. I hope some one can implement their results into a public available program (for example, Modeller, PyMol or Deep Viewer).
Direct homology modeling of phosphorylated polypeptide may not make any sense if the template used is not phosphorylated because the conformational change. But if a molecular modeling program allows to add the phosphate group on a model (similar to adding S-S bridge in Modeller) followed by MD simulation, the final model could make sense (Groban et al's paper is very encouraging).
I noticed that in the topological library of Modeller9v4, there are information for "converting (patching?) tyrosine to monoanionic phosphotyrosine (PRES TP1)", but no information on converting Thr, Ser and Asp. I wonder if any body tried to patch a model from Tyrosine to phosphotyrosine with Modeller. Is there any possibility to implement information for other residues for patching purpose?
Is there any other free program which has this functionality? Thank you for your comments and suggestions. Best regards, Xiao-Ping At 02:16 AM 10/29/2008, you wrote:
Perhaps homology modelling is not the best method. This might help: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1440919 Best of luck. ~alden Xiao-Ping Zhang wrote: > Hi, > > Many proteins are phosphorylated in vivo and and the status of their > phosphorylation correlate to their function. The residues which are > phosphorylated (Thr, Tyr or Ser) can be determined by mass spectrometry. > I wonder how to build a phosphorylated model directly or how to apply a > patch on a model to get a phosphorylated model in Modeller? > > Thank you advance for your suggestions. > > Xiao-Ping Zhang > > > > _______________________________________________ > modeller_usage mailing list > > https://salilab.org/mailman/listinfo/modeller_usage > >