Hi Michael, where did you look for creatine? My first stop would be the pdb, and when I type the word creatine in the ligand search window, I get three hits:
3A6J 3B6R 1V7Z Identification of ligand binding sites and computational docking of ligands is a bit more involved than opening both components in PyMOL. RosettaDock does a good job but has a steep learning curve. You can also do molecular dynamics (ditto). Either process will work much better if you have a rough idea where the binding site is. Identification of surface features shared between your structure and the binding sites in the three structures in the pdb could be a first step, also sequence alignment and identification of conserved residues, especially those involved in creatine binding above. Or you identify residues that when mutated abolish creatine binding in your protein. You don't say that you know the structure of your protein. If you don't have that, Phyre can quickly show if (and how much) your protein is similar to known creatine binding proteins. Best. Andreas On 14/11/2013 10:40, Michel Bielecki wrote: > Hey guys, > > I was wondering if someone could give me some information, I tried > finding it out myself but failed. I just recently started using pymol. > What I am trying to achieve: I have a protein (Sequence known), based on > experiments I know that it is a creatine transporter. My first problem > is that I can´t find a creatine.pdb anywhere. Now suppose I find it - > is it somehow possible to open both files in pymol and tell it to > find possible binding sites for my creatine molecule? > Or do I need additional plugins for that? If so - which ones? > I would be grateful for any help. > > Thanks in advance! > > Michael > > > ------------------------------------------------------------------------------ > DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps > OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access > Free app hosting. Or install the open source package on any LAMP server. > Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! > http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk > > > > _______________________________________________ > PyMOL-users mailing list ([email protected]) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/[email protected] > -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London ------------------------------------------------------------------------------ DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
