----- Forwarded message from David Farrell farrelld@ohsu.edu -----

Dear Dr. Sali,

I need some advice on some molecular modeling experiments. We have a fibrinogen peptide, VRPEHPAETEY(SO3)DSLY(SO3)PEDDL, which binds to thrombin exosite II, and we would like to use "Dock" to get an idea of the contacts between the peptide and thrombin. The problem is that although there are many solved crystal structures for thrombin, there is no published structure for the peptide. Could Modeller give predictions for the conformation of the peptide that we could then use in Dock? Or is it more likely that this short peptide is mostly a random coil that assumes an induced-fit conformation upon binding to thrombin? If so, is there any other approach to predict the structure of the bound peptide in silico?

Sincerely,

David Farrell

David H Farrell, PhD Associate Professor Dept of Pathology, L113 Oregon Health & Science University 3181 SW Sam Jackson Park Rd Portland, OR 97239 503-494-8602 503-494-2025 FAX E-mail: farrelld@ohsu.edu http://www.ohsu.edu/pathology/FacultyOHSUFarrell.htm

----- End forwarded message -----