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X-ray display one long ± helix, while Rosetta incorrectly unfolds BCscore of the lowest Rosetta score models is 0.58 vs 0.45 with
the helix C terminus for 1by0 and incorrectly breaks the helix PEP-FOLD2 but well below the average BCscore score of 0.86
for the two homologues 1usd and 1use. Note however that the for the best models. Similarly to PEP-FOLD2, native-like and
1usd and 1use structures have been solved by X-ray diffraction native models can be identified in the best five ranked
and their native structure consists of a coiled-coil tetramer suboptimal solutions, the average BCscore reaching 0.70 with
domain stabilized by interpeptide interactions. To which extent Rosetta vs 0.68 with PEP-FOLD2.
interpeptide contacts stabilize the helical conformation of the Overall from the selection of the five models of lowest
monomer remains to be determined, but we found that the 2D energy, Rosetta is able to identify near-native or native models
predictions methods Porter53 and Psi-pred54 predict a long for 42 targets and native models for 28 targets. The Rosetta
unbroken ± helix, consistent with PEP-FOLD2 prediction. score fails to identify near-native models for 1by0, 1yyb, 2kbl,
Second, one notes that the number of very high quality 2k76, 2gdl, 2ovc, 2kya, 1jrj, 2k9d, 1usd, 1vpu, 1use, 1w4e, and
models (BCscore > 0.9) obtained using Rosetta is slightly larger 1w4g, seven of whichÕà2kbl, 2gdl, 2ovc, 2kya, 1jrj, 1use,
than that obtained with PEP-FOLD2-34 versus 29. This can be 1w4gÕàare also incorrectly identified by PEP-FOLD2. The
related to the fact that PEP-FOLD2 does not include a other targets include the pairs of homologues 1use-1usd and
procedure similar to Rosetta s with multiple coarse-grained 1w4e-1w4g, 1yyb, and 1by0 for which Rosetta failed to
procedures and a final all-atom refinement procedure. generate near native models, 2k76 a miniature protein including
J dx.doi.org/10.1021/ct500592m | J. Chem. Theory Comput. XXXX, XXX, XXX-XXX
Journal of Chemical Theory and Computation Article
Table 2. Results per Target Using PEP-FOLD and Rosettaa
PEP-FOLD Rosetta
PDB best lowE best five nEq best lowE best five nEq
1by0 0.86 0.65 0.68 4.4 0.40 0.65 0.05 39.6
1yyb 0.87 0.73 0.76 2.5 0.52 0.73 -0.12 29.2
2kbl 0.71 0.37 0.44 124.9 0.69 0.37 0.43 3.6
2k76 0.88 0.26 0.81 1.3 0.69 0.26 0.55 8.1
2gdl 0.45 0.05 0.15 13.1 0.41 0.05 0.29 57.2
2l0g 0.95 0.42 0.95 2.9 0.98 0.42 0.94 1.9
2bn6 0.86 0.58 0.80 4.4 0.91 0.58 0.87 5.4
2ovc 0.52 0.49 0.45 11.3 0.25 0.49 0.16 43.9
1bwx 0.93 0.70 0.78 11.2 0.90 0.70 0.63 8.5
2kya 0.56 0.26 0.26 92.2 0.45 0.26 0.21 21.9
1wy3 0.91 0.83 0.61 1.9 0.97 0.83 0.96 2.4
1wr3 0.94 0.80 0.88 24.7 0.92 0.80 0.89 1.2
1wr4 0.94 0.91 0.89 27.4 0.93 0.91 0.90 1.2
2ki0 0.89 0.63 0.80 5.3 0.94 0.63 0.90 1.0
1e0m 0.88 0.66 0.78 35.5 0.90 0.66 0.87 1.1
1e0n 0.92 0.68 0.84 85.8 0.95 0.68 0.92 1.0
1yiu 0.84 0.64 0.73 21.8 0.91 0.64 0.83 1.1
1bhi 0.82 -0.28 0.32 165.2 0.93 -0.28 0.88 162.3
1i6c 0.85 0.69 0.78 43.7 0.83 0.69 0.68 1.3
1jrj 0.85 0.11 0.55 4.3 0.63 0.11 0.42 10.2
2ysc 0.86 0.64 0.77 166.5 0.85 0.64 0.79 1.4
1e0l 0.92 0.28 0.85 70.0 0.89 0.28 0.78 5.8
2ysf 0.93 0.60 0.86 83.5 0.92 0.60 0.88 1.1
2ysg 0.93 0.35 0.90 48.0 0.91 0.35 0.83 2.8
2ysh 0.89 0.20 0.78 33.5 0.92 0.20 0.87 1.2
2ysi 0.85 0.78 0.77 50.1 0.79 0.78 0.75 1.3
1k1v 0.92 0.02 0.89 3.7 0.94 0.02 0.90 2.5
1wr7 0.95 0.88 0.94 68.0 0.93 0.88 0.91 1.2
1ywj 0.91 0.86 0.88 119.4 0.88 0.86 0.83 3.2
1ymz 0.93 0.81 0.88 49.0 0.94 0.81 0.92 3.0
2dmv 0.93 0.75 0.86 114.4 0.93 0.75 0.91 6.0
2k9d 0.82 0.60 0.72 5.5 0.68 0.60 0.57 2.2
2p81 0.96 0.59 0.90 14.0 0.93 0.59 0.74 4.3
1f4i 0.95 -0.49 0.90 5.6 0.98 -0.49 0.98 1.1
1p9c 0.86 0.52 0.64 37.1 0.86 0.52 0.74 137.9
1usd 0.87 0.30 0.79 3.6 0.47 0.30 0.35 15.6
1vpu 0.63 -0.57 -0.56 47.6 0.70 -0.57 0.55 3.5
3e21 0.91 0.78 0.76 4.4 0.99 0.78 0.98 2.1
1pv0 0.95 -0.39 0.46 6.2 0.94 -0.39 0.94 4.5
2e5t 0.92 0.42 0.71 2.9 0.97 0.42 0.97 7.0
2jnh 0.97 0.75 0.75 15.2 0.94 0.75 0.72 1.9
2l4j 0.90 0.69 0.85 108.7 0.92 0.69 0.90 2.3
1dv0 0.94 0.83 0.75 3.5 0.98 0.83 0.98 1.4
1use 0.87 0.50 0.49 7.8 0.55 0.50 0.31 45.6
1w4e 0.94 0.69 0.65 91.3 0.94 0.69 0.05 4.6
1w4g 0.90 -0.06 0.10 48.9 0.91 -0.06 0.01 2.9
2btg 0.96 0.91 0.83 36.4 0.94 0.91 0.79 1.8
2ekk 0.97 0.51 0.86 7.2 0.98 0.51 0.98 5.5
2wxc 0.91 0.51 0.83 36.5 0.90 0.51 0.73 2.5
1ify 0.85 -0.35 -0.16 8.7 0.97 -0.35 0.95 1.6
1nd9 0.73 0.64 0.65 5.6 0.69 0.64 0.68 1.4
2j8p 0.92 -0.72 0.81 1.4 0.88 -0.72 0.82 3.5
2ysb 0.88 0.25 0.81 170.6 0.87 0.25 0.76 11.6
2zaj 0.80 0.57 0.67 175.2 0.83 0.57 0.74 104.1
1w4h 0.93 0.89 0.91 88.7 0.93 0.89 0.74 6.3
1pgy 0.89 0.60 0.81 12.1 0.93 0.60 0.83 1.6
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