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


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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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