Google 2D-GraLab. Very good at showing detailed interface contacts along protein sequences. To my knowledge, there is no way to include a non protein ligand. But the source code is available on request and if you succeed to modify the program, please let us know. HTH,
Nadir Mrabet Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-964 University of Lorraine, Nancy School of Science and Technology and School of Medicine 9, Avenue de la Foret de Haye 54500 Vandoeuvre-les-Nancy, France Tel. (direct) : +33 (0)3.83.68.32.73 Tel. (secretary) : +33 (0)3.83.68.32.92 Fax. : +33 (0)3.83.68.32.79 Email : Nadir.Mrabet <at> univ-lorraine.fr ----- eugene krissinel <[email protected]> a écrit : > This is the kind of things MG was designed to do -- Eugene On 4 Jun 2013, at > 15:18, Tobias Beck wrote: Dear all, I would like to visualize the interface > of a protein-protein complex. The complex formation is modulated by a ligand > that upon binding alters the overall structure of one protein, which then in > turn forms the complex with the second protein (structure of the complex is > known). Ligand binding does not seem to induce a discrete conformational > switch, rather a subtle alteration of the contact interface. The isolated > structure of the first protein without the ligand is known as well. In > addition to depicting the structural difference in conventional ways I was > thinking to draw some kind of stretched out topology map of the surface that > is interacting - first the surface from the isolated protein, then the > surface as it is found in the complex and then maybe some kind of difference > map... Does anybody have some suggestions how to do this? I would prefer to > do some kind of stretched out surface (basically a rectangle of the region of > interest) and show "mountains and valleys" and their change, but not sure if > this is feasible. Thanks for any advice! Best wishes, Tobias. -- > ___________________________________________ Dr. Tobias Beck ETH Zurich > Laboratory of Organic Chemistry Wolfgang-Pauli-Str. 10, HCI F 322 8093 > Zurich, Switzerland phone: +41 44 632 68 65 fax: +41 44 632 14 86 web: > http://www.protein.ethz.ch/people/tobias > ___________________________________________ -- Scanned by iCritical.
