I guess you would require some kind of titration event modeling first. The first thing that would come up to my mind with regards to pH dependent properties of amino acids would be to somehow link Propka into an MD simulation, i.e. whenever you change the pH, you recompute the protonation states of the residues and suject the new file to the MD, could be interesting actually.
Martin On 18.06.11 23:59, Eric Martz wrote: > Does anyone know of an animation simulation (atomic coordinates) for > changes in 3D protein conformation (or amino acid conformation) due > to changes in pH? > > Thanks, -Eric > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Eric Martz, Professor Emeritus, Dept Microbiology > U Mass, Amherst -- http://Martz.MolviZ.Org > > Top Five 3D MolVis Technologies http://Top5.MolviZ.Org > FirstGlance, used by Nature - http://firstglance.jmol.org > 3D Wiki with Scene-Authoring Tools http://Proteopedia.Org > Biochem 3D Education Resources http://MolviZ.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > Atlas of Macromolecules: http://atlas.molviz.org > Workshops: http://workshops.molviz.org > World Index of Molecular Visualization Resources: http://molvisindex.org > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List (molvis-list): http://list.molviz.org > Protein Explorer - 3D Visualization: http://proteinexplorer.org > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > ------------------------------------------------------------------------------ EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
