Table 1.
2002 vs. best smooth 2010 rotamer libraries: benchmarking based on SCWRL4 side-chain conformation prediction accuracy.
| Categ | TRP | PHE | GLN | GLU | TYR | SER | ARG | HIS | LEU | MET | CYS | THR | ASP | ILE | VAL | LYS | ASN | PRO | ALL | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Best ’10 | χ1 | 94.1 | 98.1 | 85.0 | 81.0 | 97.1 | 75.4 | 83.1 | 93.5 | 96.4 | 90.2 | 93.2 | 94.3 | 90.5 | 98.5 | 96.9 | 82.8 | 91.7 | 87.1 | 90.15 |
| Old ’02 | 92.9 | 97.6 | 84.6 | 80.1 | 96.5 | 74.3 | 83.3 | 93.9 | 95.9 | 90.4 | 92.8 | 94.0 | 90.6 | 98.4 | 96.7 | 82.6 | 91.7 | 87.3 | 89.83 | |
| Δ(Best, Old) | +1.2 | +0.5 | +0.4 | +1.0 | +0.6 | +1.1 | −0.2 | −0.4 | +0.5 | −0.2 | +0.4 | +0.4 | −0.1 | +0.1 | +0.2 | +0.3 | 0.0 | −0.2 | +0.32 | |
| Best ’10 | χ1+2 | 84.6 | 96.6 | 71.1 | 68.0 | 94.8 | 72.9 | 66.4 | 91.9 | 81.9 | 84.7 | 91.0 | 72.3 | 76.7 | 83.9 | 81.73 | ||||
| Old ’02 | 78.9 | 93.7 | 71.0 | 67.5 | 92.9 | 72.5 | 64.6 | 91.2 | 81.9 | 83.8 | 90.6 | 72.5 | 77.0 | 84.3 | 81.01 | |||||
| Δ (Best, Old) | +5.7 | +2.9 | +0.1 | +0.6 | +1.9 | +0.5 | +1.8 | +0.8 | 0.0 | +0.9 | +0.4 | −0.2 | −0.3 | −0.4 | +0.72 | |||||
| Best ’10 | χ1+2+3 | 48.8 | 52.4 | 51.0 | 64.2 | 58.4 | 54.01 | |||||||||||||
| Old ’02 | 44.5 | 49.3 | 49.6 | 62.5 | 58.7 | 52.05 | ||||||||||||||
| Δ (Best,Old) | +4.2 | +3.1 | +1.5 | +1.7 | −0.3 | +1.96 | ||||||||||||||
| Best ’10 | χ1+2+3+4 | 38.1 | 39.9 | 38.99 | ||||||||||||||||
| Old ’02 | 36.3 | 39.6 | 38.01 | |||||||||||||||||
| Δ (Best,Old) | +1.8 | +0.2 | +0.98 | |||||||||||||||||
| Best ’10 | χall | 89.3 | 97.4 | 68.3 | 67.1 | 96.0 | 75.4 | 61.3 | 80.0 | 94.1 | 78.8 | 93.2 | 94.3 | 87.6 | 94.8 | 96.9 | 63.4 | 84.2 | 85.5 | 83.72 |
| Old ’02 | 85.9 | 95.7 | 66.7 | 65.6 | 94.7 | 74.3 | 60.4 | 79.2 | 93.5 | 78.3 | 92.8 | 94.0 | 87.2 | 94.5 | 96.7 | 63.4 | 84.3 | 85.8 | 83.04 | |
| Δ (Best,Old) | +3.4 | +1.7 | +1.6 | +1.5 | +1.2 | +1.1 | +0.9 | +0.7 | +0.6 | +0.5 | +0.4 | +0.4 | +0.4 | +0.3 | +0.2 | 0.0 | −0.2 | −0.3 | +0.67 | |
The performances of the new 2010 rotamer libraries were compared with the 2002 rotamer library. SCWRL4 was run on a set of 379 high-resolution proteins used previously (Krivov et al, 2009). The flexible rotamer model (FRM) of SCWRL4 was used, and crystal symmetry was used in the calculations (all side chains in all copies of the asymmetric unit were calculated simultaneously). Accuracy was evaluated on all side chains in the proteins excluding those with electron density in the bottom 25th percentile for each residue type. A predicted side-chain χ is considered correct if its value lies within 40° from its experimental value. For each residue type the 2002 and 2010 accuracies are provided for each individual χ angle. χall is an absolute average of all degrees of freedom for each residue (see Supplementary Material). ALL is an average accuracy among all 18 standard residue types.