Readme file for supplementary materials of the paper: 

Empirical potential function for simplified protein models: Combining
contact and local sequence-structure descriptors Proteins: structure,
function and bioinformatics, 
by Jinfeng Zhang, Rong Chen and Jie Liang, to be published in Proteins, 2005

angle_cluster.dat is clustered discrete state angles. Detailed
descriptions are given in the file.

calsp.txt is potential function CASLP with 610 descriptors. There is
only one line in the file containing 610 coefficients for the 610
descriptors. The first 400 numbers are for local sequence structure
descriptors (this is the same for RCALSP1 and RCALSP2) and the last
210 parameters are for contact descriptors.

rcalsp1.txt is potential function RCALSP1 with 400 local
sequence-structure descriptors 55 contact descriptors.

rcalsp2.txt is potential function RCALSP2 with 400 local
sequence-structure descriptors and 165 contact descriptors in three
contact order bins. Please see the paper for details.

The way to determine the index of the descriptors is as following: 

For the first 400 local sequence-structure descriptors (from 0 to 399),
    N = (5*s_i+a_i)*20 + (5*s_{i+1} + a_{i+1}), 
where N is the index of the descriptor, s_i and s_{i+1} are the
discrete state (0-3) at position i and i+1, respectively, a_i and
a_{i+1} are the geometricly simplfied alphabet type (0-4) at position
i and i+1, respectively.

For contact descriptors (starting from 400):
    N = 20 * R_i + R_j, 
where N is the index of descriptor, R_i and R_j are the integer
representation of the amino acid type at position i and j,
respectively. Residue i and j form a contact in this case.

The amino acid and their integer representation used in determining the
descriptor index is as following:

Amino acid integer representation for 20 letter alphabet for contact
descriptors in CALSP:
A 0
C 1
D 2
E 3
F 4
G 5
H 6
I 7
K 8
L 9
M 10
N 11
P 12
Q 13
R 14
S 15
T 16
V 17
W 18
Y 19

Simplified alphabet based on contact propensities, where 20 amino acid
alphabet is simplified to an alphabet with 10 letters, for RCALSP1 and
RCALSP2:
A 8
C 0
D 1
E 1
F 6
G 9
H 4
I 5
K 2
L 5
M 6
N 3
P 4
Q 3
R 2
S 3
T 3
V 5
W 7
Y 7

Geometrically simplified alphabet with 5 letters for local
sequence-structure descriptors used in all potential functions:
A 1
C 0
D 4
E 1
F 0
G 2
H 1
I 0
K 1
L 0
M 0
N 4
P 3
Q 1
R 1
S 1
T 1
V 0
W 0
Y 0