Respected sir,
I modelled number of proteins by basic modelling. After basic modelling during procheck evaluation the residues in most favorable region is generally above 90% but after loop refinement the residues in most favorable region comes below 90%. Please kindly inform me what may be the region for this.
Also after energy minimization the the percentage of residue in most favorable region decreses.
I will be grateful to listen from u regarding my query
Thanking you,
Dibyabhaba Pradhan Project Assistant, SVIMS BIC, India
On 10/31/08, Xiao-Ping Zhang xpzhang@ucdavis.edu wrote: > 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 > > > modeller_usage@salilab.org > > > https://salilab.org/mailman/listinfo/modeller_usage > > > > > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >