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The authors have demonstrated that a short, all-atom minimization with fixed C&…


Biology Articles » Methods & Techniques » Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field » Tables

Tables
- Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field

Table 1
The CABS decoys set
PDB ID
% α
% β
L
% of low energy structures
2gr8A
16
50
78
99
2cklA
44
14
98
93
2gmkA
19
41
103
75
2gu3A
19
48
128
79
2grrB
64
0
157
92
2cl4X
52
2
250
68
2cjpA
45
16
320
38
Particular columns contain: the PDB code, the fraction of alpha helices, the fraction of beta strands, the protein length and the fraction of correctly built structures (where the minimization did not result in abnormal high energy values).
Table 2
The 7 protein subsets from the MOULDER testing set
PDB ID
SS type
L
RMSD range
Median RMSD
avg.ΔRMSD (best, rank.)
ΔRMSD
2mtaC
α
81
2.2–42.7
6.7
0.56 (0.30, 5)
0.26
1onc_
α, β
101
2.2–22.8
10.5
0.37 (0.25, 8)
0.30
1bbhA
α
127
2.5–20.8
6.5
0.51 (0.05, 17)
0.76
1mdc_
β
130
1.9–16.4
9.3
0.37 (0.13, 8)
0.02
1dxtB
α
143
2.0–34.1
7.2
0.56 (0.31, 3)
0.08
2fbjL
β
210
2.4–22.5
8.8
1.51 (0.32, 19)
0.53
2cmd_
α, β
310
2.5–20.2
5.8
1.26 (0.31, 13)
1.58
Particular columns contain: the PDB code, the secondary structure type, the protein length, the range of Cα RMSD (Å), the median of RMSD (Å), the average ΔRMSD of our method, in the brackets: the average ΔRMSD of the best method [12] and a ranking – the number of methods that outperformed our procedure (23 individual assessment methods were tested, SVMod that uses a composite score from the individual methods was not taken into account [12]), the ΔRMSD on the whole subset.

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