Ed Pozharski wrote:
Does anyone know of a tool that would generate a protein molecule
backbone from a set of phi/psi angles?
I actually had written my own code to do this eons ago, but those were
days of Matlab. My actual question is if in a particular protein the
conformational change observed upon substrate binding can be accounted
for by half a dozen residues changing their backbone conformation. I
only expect to do it once, and thus trying to save time and not
translate my old code (looks more like a cipher now).
The underlying assumption of such a program is that the phi, psi (and
omega) angles define the structure, and vice versa. So if you have the
before and after structures, you sort of have the answer already-
given that change in dihedrals, you will get that change in structure,
although I'm not sure if it makes sense to ask whether the strutural
chage results from the change in dihedrals or vice versa.
I guess you want to keep all dihedrals the same except the half-dozen
suspects, and see if you get the same change. dihedrals elsewhere would
be expected to change to reoptimize to new contacts and avoid clashes,
but maybe the principle change could still be recognized with the rest
of the molecule frozen.
I have such a code (fortran) that reads a list of phi,psi angles and
makes the corresponding backbone (poly gly or polyala I think).
Unfortunately it sets all omega angles to exactly 180? (trans), and that
by itself may make a significant change in conformation.
http://sb20.lbl.gov/berry/for/construct.f
written for g77 but gfortran seems to compile.
input file format is 1 line for each residue: residue #, phi, psi
1 -49 -26
2 -49 -26
3 -49 -26
4 -49 -26
5 -49 -26
6 -49 -26
7 -49 -26
8 -49 -26
9 -49 -26
10 -49 -26
11 -49 -26
12 -49 -26
o
usage:
construct < 3-10helix.inp
new file is called construct.pdb
chain is A
EAB
Cheers,
Ed.
--
After much deep and profound brain things inside my head,
I have decided to thank you for bringing peace to our home.
Julian, King of Lemurs
