EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments

BMC Bioinformatics

Table 2 Mean rank evaluation of the structure-dependent EvDTree substitution scores and comparison with other scoring functions.

Amino acid	DT0^b	DT^a	GON^a	B62^a	Fug^a
A	7.93	7.33	8.21	8.34	7.51
C	10.62	10.60	11.01	11.86	10.19
D	6.48	6.41	6.85	6.59	6.48
E	6.83	6.73	6.92	6.95	6.79
F	6.66	6.58	7.04	6.86	7.01
G	7.14	7.14	7.16	7.20	7.00
H	8.18	8.05	8.29	7.98	7.97
I	5.65	5.38	5.88	5.72	5.58
K	6.97	6.93	6.88	6.86	6.81
L	6.71	6.39	6.58	6.69	6.52
M	5.68	5.68	6.01	5.84	5.87
N	6.82	6.73	7.20	7.03	6.90
P	7.15	7.15	7.58	7.80	7.33
Q	6.74	6.74	7.08	7.28	7.29
R	7.46	7.24	7.41	7.41	7.21
S	6.43	6.32	7.03	6.73	6.67
T	6.61	6.61	7.21	6.74	7.00
V	6.50	6.28	6.65	6.38	6.36
W	8.03	7.61	8.81	9.04	7.63
Y	8.38	8.11	9.15	8.82	8.02
J	7.12	7.12	8.17	7.48	7.16
Average	6.90	6.74	7.15	7.06	6.87

^aMean rank evaluation of the EvDTree (DT), Gonnet (Gon), Blosum62 (B62) and FUGUE (Fug) substitution scores. ^bMean rank evaluation of EvdTree0 (DT0), i.e. scores inferred from the root clusters before structural classifications. Bold numbers indicate the best values among the methods.

ISSN: 1471-2105