Table 4.
The root-mean-squared distance (RMSD) from the native structure of the best structure in top five clusters of three independent runs (top 15) by an energy function only, with restraints around ideal angles of predicted helical and strand residues (secondary structure restraints), around predicted real-value angles of predicted helical and strand residues, and around predicted real-value angles of all residues.
| PDB IDa | Lb | α/β/coil (%)c | Q60° (%)d | Q3 (%)e | Best RMSD in Top 15 in Å | |||
|---|---|---|---|---|---|---|---|---|
| No Res.f | Ideal α&βg | Real α&βh | Alli | |||||
| 1b72 | 49 | 71/0/29 | 66.6 | 67.3 | 4.9 | 5.3 | 5.1 | 6.5 |
| 1shf | 59 | 0/42/58 | 86.0 | 79.7 | 9.1 | 8.5 | 6.9 | 3.1 |
| 1tif | 59 | 24/37/39 | 89.5 | 84.7 | 8.5 | 6.2 | 4.5 | 4.2 (3.4j) |
| 2reb | 60 | 62/22/16 | 91.4 | 85.0 | 6.6 | 3.2 | 5.6 | 3.2 |
| 1r69 | 61 | 71/0/29 | 93.2 | 96.7 | 6.7 | 9.0 | 6.2 | 2.0 |
| 1csp | 67 | 0/55/45 | 86.2 | 77.6 | 10.4 | 7.3 | 6.1 | 4.9 |
| 1di2 | 69 | 42/33/25 | 92.5 | 95.7 | 11.6 | 3.8 | 6.5 | 3.2 |
| 1n0u | 69 | 45/28/27 | 98.5 | 87.0 | 9.4 | 4.1 | 4.2 | 4.1 |
| 1mla | 70 | 37/37/26 | 91.2 | 90.0 | 8.0 | 3.0 | 3.3 | 4.4 |
| 1af7 | 72 | 71/0/29 | 95.7 | 97.2 | 5.8 | 6.1 | 4.9 | 3.1 |
| 1ogw | 72 | 26/32/42 | 90.0 | 79.2 | 8.0 | 6.8 | 6.5 | 6.0 |
| 1dcj | 73 | 36/32/32 | 90.1 | 91.8 | 8.9 | 4.2 | 4.1 | 3.2 |
| 1dtj | 74 | 41/27/68 | 83.3 | 83.8 | 10.2 | 6.3 | 5.2 | 5.1 |
| 1o2f | 77 | 48/29/23 | 84.0 | 81.8 | 9.5 | 6.6 | 5.7 | 9.7 |
| 1mky | 81 | 35/25/40 | 91.1 | 86.4 | 11.9 | 7.0 | 4.5 | 8.0 (5.2j) |
| 1tig | 88 | 39/35/26 | 82.6 | 75.0 | 10.7 | 11.7 | 10.5 | 10.6 |
| Median: | 40/27/33k | 88.2k | 84.9k | 9.0 | 6.3 | 5.4 | 4.3 | |
| Success Rate (RMSD<6Å)l: | 2/16 | 6/16 | 10/16 | 12/16 | ||||
Protein Data Bank Identification Number (a dataset of Ref. (Bradley et al., 2005)).
Chain length (Bradley et al., 2005).
Fractions of native helical, strand and coil residues.
Fraction of residues for which predicted angles are within 60° from their native values for both ϕ and ψ angles.
The accuracy of secondary structure prediction by an improved version of SPINE (Dor and Zhou, 2007a; Faraggi et al., 2009). The best structure (in RMSD) in top five clusters of three independent runs (top 15)
without torsion angle restraints (DFIRE plus hydrogen bonding only).
The energy function plus restraints around ideal angles of predicted helices and strands.
The energy function plus restraints on predicted real values of torsion angles of predicted helical and strand residues only.
The energy function plus restraints on all residues.
A native cis-conformation is assigned to Pro 54 in 1tif and Pro 394 (ω = 0°) in 1mky.
Average.
The success rate: the number of proteins having a correct structural topology (RMSD<6Å) ranked within top 15.