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

BMC Bioinformatics

Table 3 Mean rank evaluation of small disulfide-rich proteins using standard and specific scoring functions.

Amino acid	DT^a	DS0^a	DS^a	Fug^a	Gon^a	B62^a
A	8.16	8.59	7.71	8.39	8.85	8.83
C	9.84	11.60	8.09	10.42	11.8	11.72
D	6.85	7.50	7.31	6.90	7.12	7.01
E	6.70	7.57	7.22	6.89	6.88	6.89
F	8.58	8.77	7.58	10.14	9.79	9.86
G	8.03	7.74	7.35	7.48	7.40	7.46
H	7.99	8.04	7.51	8.00	7.72	8.09
I	7.74	8.55	7.28	7.82	8.36	8.19
K	7.47	8.07	7.56	7.49	7.59	7.36
L	9.13	9.41	8.34	9.25	9.70	9.90
M	9.74	9.04	7.33	8.95	9.16	8.87
N	7.57	8.14	8.09	7.411	8.40	8.02
P	8.20	8.41	8.00	8.11	8.70	8.56
Q	6.88	7.94	7.81	7.35	7.38	7.38
R	7.93	8.20	6.96	7.84	7.99	8.11
S	7.56	7.55	7.55	7.56	8.29	8.17
T	8.14	8.61	7.63	8.53	9.40	8.91
V	8.30	7.69	7.69	7.82	8.76	8.48
W	8.78	7.46	7.45	8.20	9.03	8.82
Y	8.61	8.59	7.53	8.76	9.77	9.32
Average	7.90	8.27	7.59	8.02	8.44	8.38

^aMean rank evaluation using the EvDTree (DT), EvDTreeDS0 (DS0), EvDTreeDS (DS), FUGUE (Fug), Gonnet (Gon) and Blosum62 (B62) substitution scores. Bold numbers indicate the best values among the methods.

ISSN: 1471-2105