Table III. Recoveries and energies of weight optimized standard + unfolded state energy functions.
This table reports the native sequence recoveries, largest hydrophobic patch area and total hydrophobic surface area averages for various weight optimized energy functions. The energy functions tested include a reweighted standard energy function that replaces the reference energies with the unfolded state energy term (“standard, no refE + unfoldedE”) and the same energy function with the hpatch-SASA score (“standard, no refE + unfoldedE, hpatch-SASA”). Both of the reweighted energy functions were optimized for native sequence recovery alone. Extra χ1 and χ2 rotamers used for all residues (−ex1 −ex2 −extrachi_cutoff 0).
| recovery | avg QUILT patch −ep 1.4 -R |
% hp on surface |
avg total hASA −ep 1.4 |
hpatch weight |
|||
|---|---|---|---|---|---|---|---|
| energy function | core | overall | surface | ||||
| natives | --- | --- | --- | 476 | 27.8 | 1100 | --- |
| standard, no refE + unfoldedE, training | 55.9 | 32.8 | 17.9 | 1403 | 48.1 | 1837 | --- |
| standard, no refE + unfoldedE, hpatch-SASA, training | 50.6 | 31.8 | 18.9 | 424 | 29.3 | 1024 | 0.5 |
| standard, no refE + unfoldedE, test | 47.7 | 30.5 | 21.0 | 1479 | 46.4 | 1844 | --- |
| standard, no refE + unfoldedE, hpatch-SASA, test | 48.4 | 29.8 | 19.9 | 464 | 30.3 | 1064 | 0.5 |