Dear Crystallographers,
I am trying to determine the binding register of a helical peptide into a
binding groove of a protein of known structure. There are several known
peptide-protein complex structures of this protein in the PDB (each
containing the same protein but different peptides). None of these peptides,
however, is very similar in sequence to my peptide. Since I have strong
biochemical evidence that my peptide indeed binds tightly, I am looking for
a way to determine the actual (or optimal? Are those different?)
mode/register of binding. I was envisioning a brute force iteration through
all possible register-shifts followed in each case by energy minimization.
Then a plot of register versus [some energy parameter] would show which was
the correct register. Can anybody suggest a good piece of software for this
(with or without modification/scripting)?
Thanks,
Jacob Keller
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: [log in to unmask]
*******************************************
|