----- Forwarded message from David Farrell <> -----
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:
http://www.ohsu.edu/pathology/FacultyOHSUFarrell.htm
----- End forwarded message -----