H DOSZ010103
D An amino acid similarity matrix based on the THREADER force field
(Dosztanyi-Torda, 2001)
R PMID:11524370
A Dosztanyi, Z. and Torda, A.E.
T Amino acid similarity matrices based on force fields
J Bioinformatics. 17, 686-699 (2001)
* #SM_THREADER
* #An amino acid similarity matrix based on the THREADER force field (Jones, DT et al.Nature, 358,86-89).
* #Supplementary material
* #http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices/SM_THREADER
* #Zsuzsanna Doszt?yi and Andrew E. Torda
* #Amino acid similarity matrices based on force fields
* #The amino acids are ordered according to the first principal component of the SM_SAUSAGE matrix.
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
10.0    -0.2    -1.2    -2.8     3.8     0.6    -1.0     0.9     0.2     5.1     4.5    -1.4     3.9     1.9    -0.9     1.8     1.6     0.5     1.8     5.5
2.3     8.1    -0.4    -1.6    -0.6     2.9     1.0    -1.9     1.8     0.5     1.8     3.6     1.7     0.4    -2.1     0.2     0.7    -0.5     1.7     1.0
1.5     0.3     6.4     1.9    -0.3     1.2     0.6     0.5     2.0    -0.4    -1.1     0.5     0.2    -1.9    -1.3     1.6     1.0    -2.4    -0.4    -0.6
0.7    -0.4     2.2     7.3    -2.3     1.5     2.7    -0.4     0.2    -1.6    -1.3    -0.1    -1.7    -3.0    -0.4     0.9     0.2    -3.4    -1.4    -1.8
2.7    -3.0    -2.4    -4.9    16.3    -2.4    -4.1    -1.6    -0.9     4.0     3.7    -4.2     2.2     2.7    -3.6    -0.4     0.5    -1.2     1.0     4.6
3.5     3.2     0.8     0.6     0.0     8.4     3.3    -1.0     2.7     1.2     2.6     3.1     3.4    -0.6    -0.2     1.3     0.8     1.2     1.6     0.7
3.0     2.2     0.8     2.4    -0.6     4.1     7.0    -1.9     1.6    -0.3     1.0     2.3     1.1    -0.4    -0.2     0.4     0.7    -1.0     0.2     0.2
2.0    -2.2    -0.1    -1.3    -1.0    -1.3    -3.0     7.8    -0.9    -1.2    -1.4    -2.2    -0.9    -1.9    -1.5     0.6    -0.9    -1.7    -1.3    -1.3
1.4     1.1     0.8    -1.4     0.4     1.8    -0.2    -1.0     9.9     0.5     1.4    -0.2     2.1     2.0    -1.6    -0.2    -0.4    -0.6     4.1     0.3
4.1    -2.9    -3.8    -5.9     4.8    -2.4    -5.7    -2.5    -1.2    13.2     9.8    -4.7     7.4     6.3    -3.1    -2.2     1.1     1.6     4.0    11.8
3.6    -1.4    -4.3    -5.4     4.2    -0.8    -3.9    -2.7    -0.4     9.7    12.5    -3.9     8.3     6.8    -3.8    -2.1     0.9     2.3     3.8     8.2
2.7     4.6     0.8    -0.3    -0.7     3.9     2.4    -1.0     1.6     0.4     0.8     6.5     1.0    -1.3    -0.2     1.2     0.6    -1.1     0.2     0.0
4.3    -0.4    -2.2    -4.9     3.6     1.2    -2.5    -1.7     1.3     8.7     9.7    -2.5    11.4     5.2    -2.8    -1.0     0.9     2.7     4.1     7.2
1.8    -2.0    -4.4    -6.3     3.8    -3.1    -4.3    -2.6     1.1     7.0     7.6    -5.1     4.8    12.4    -3.8    -2.2    -0.1     4.4     7.6     5.8
0.3    -2.1    -1.5    -0.8    -2.9    -0.4    -0.7    -1.2    -1.1    -1.5    -2.4    -0.9    -1.7    -2.7     8.7    -0.4    -0.2    -3.1    -1.9    -1.5
3.5     0.0     0.9    -0.3     1.3     0.9    -0.8     0.6     0.3     0.4     0.4    -0.1     0.6    -0.4    -0.6     4.9     2.8    -2.0     0.1     1.1
2.9     0.1    -0.1    -1.4     2.1    -0.0    -1.1    -1.0    -0.3     3.2     2.9    -1.1     2.0     1.1    -0.6     2.4     5.8    -0.7     0.7     3.9
1.5    -1.8    -4.2    -5.9     0.6    -0.3    -3.8    -2.0    -0.7     3.5     4.3    -3.9     3.5     5.5    -3.7    -3.0    -1.2    16.0     5.4     3.1
2.2    -0.1    -2.5    -4.2     2.4    -0.4    -3.1    -1.9     3.6     5.4     5.1    -3.0     4.3     8.2    -2.9    -1.3    -0.2     4.9    10.8     5.1
4.6    -2.2    -3.8    -5.9     5.4    -2.6    -4.9    -2.5    -1.4    11.9     8.4    -4.8     6.1     5.1    -3.0    -1.4     2.0     1.3     3.8    12.7
//