Date: Mon, 19 Nov 2007 14:45:30 +0000
To: Yang Zhang <yzhang@ku.edu>
Subject: I-TASSER potentials again

Dear Yang,

I have a few more questions about the potential. I believe these are
the last bits needed to implement the I-TASSER potential and it would
be great if you kindly find some time to dispel my doubts.

1) Are you using centroid (geometrical center) or real center
of mass taking into account the weight of each type of side chain?

2) How do you calculate the radius of gyration? Is it just the
estimated value of 2.2*N^0.38? If it's a real distance, is it
measured using just side chain centers of mass, C-alphas or maybe both?

3) How the side chain coordinates from 2-rotamer library are
chosen? I know that first vector is for extended and second for compact
local structure but how extend/compact is decided? Are you using here
the secondary structure prediction (H is compact, else extended) or
maybe r(i,i+2) distance like in E13 potential?

4) How the potential is calculated when the residue neighbourhood is
too small to follow the equations (like at the beginning/end of the
sequence)? Are the terms impossible to compute just ignored (equal to
zero) or some defaults are assumed?

5) How exactly the local handedness of the three consecutive residues is
decided? Is it based on angles between CA-CA vectors being within some
range?

6) How the length of principal axes of the protein ellipsoid are being
determined? Is it just half distance between max and min coordinates
for each dimension?

Hope to hear from you soon and thanks in advance for clarifying the
method.