Date: Mon, 3 Sep 2007 18:42:52 +0100
To: Yang Zhang <yzhang@ku.edu>
Subject: I-TASSER energy potential questions

Dear Prof. Zhang,

I am very grateful for providing the potentials. I have spent some time
analysing them trying to learn how they were used in I-TASSER, but some
aspects still remain unclear for me.

I would appreciate if you were so kind and answer the following
questions to help me understand the details needed to implement the
I-TASSER force field.

1) What are the distance "bins" used for r13, r14 and r15 potentials?

There are 2 values for r13. Do they correspond to bins: < 4Å, > 4Å?
There are 3*8=24 values for r14. Do the correspond to bins in
range(-12Å,12A) with step 1Å? The r14 potential also seems to be
chirality depended (probably half is used for the left, half for the
right-handed conformations).
They are 2*8=16 values for r15 . Do they correspond to bins
in range(1Å,8Å) with step 0.5Å?

2) How is the final potential for r14 and r15 decided?

I know it is a combination of general (r1x) and secondary structure
specific potential (r1xe/r1xh). Is this just an arithmetic mean?

3) Are the short range potentials E'12 to E'15 for side chain
interactions from TOUCHSTONE-II article used by I-TASSER?

As TASSER articles mention modification in the short range force field
I guess that since you did not list them on the web site, they might be
not used anymore to calculate E_short. Is that correct?

4) How are the contact cutoff values related to R_min and R_max from
TOUCHSTONE-II force field?

I guess in I-TASSER the fixed 3.25Å hard core and range(3.25Å,5Å) soft
core is not used anymore. The comments in potential file mention
addition of 2.5 standard deviation to the mean. Is that a soft core
range now with the mean being hard core diameter?

5) What is the meaning of two groups of quasi (pairwise
orientation-dependent) potentials?

The 2D matrix of values is given for each pair of amino acids and
parallel, anti-parallel and perpendicular orientations. However,
instead of 3 matrices there are 6 of them. What is the meaning of
this two groups? Is it dependency on predicted secondary structure?

6) How to interpret the profile potential?

For each amino acid 9 matrices of 9x9 values are given, so it looks as
the 3D matrix for parallel, anti-parallel and perpendicular residues in
contact. What "bins" are used here? Is it just the range(0,8)?

Thank you again for your kind help.
-- Best regards,