Table 1. Performance of RN (odds ratio) metric in rotamer library design for αAA residues.
VDW=90% ε = 20 |
VDW=90% ε = 10 |
VDW=95% ε = 20 |
VDW=95% ε = 10 |
VDW=100% ε = 20 |
VDW=100% ε = 10 |
|
---|---|---|---|---|---|---|
False Negatives | ||||||
α-Helix | 3 | 6 | 5 | 7 | 5 | 8 |
β-Sheet | 2 | 3 | 4 | 4 | 5 | 5 |
False Positives | ||||||
α-Helix | 0 | 0 | 0 | 0 | 0 | 0 |
β-Sheet | 5 | 5 | 1 | 1 | 1 | 1 |
VDW is the vdw radii-scaling factor, ε is the distance-dependent dielectric constant. False positives and false negatives are listed when compared to knowledge-based αAA rotamer library of 48 rotameric states. ‘Good’ (positive) and ‘bad’ (negative) rotamers have odds ratio RNobs of >0.1 and <0.01 respectively.