Fig. 4: Score function comparison for one protein and different loop modeling protocols.

The protocols are A cyclic coordinate descent—CCD, B kinematic closure—KIC, C KIC with fragments, and D next-generation KIC—NGK. Score functions are sorted from oldest to newest (left to right) and the models are colored in gray as the native (PDB) structure, then according to the score functions in order: yellow—score12, green—talaris13, cyan—talaris14, and teal—ref2015. This figure shows a particularly interesting example, which is not necessarily representative of other targets. Interesting for this target are the differences in the energy landscapes that are sampled and the presence of a second, incorrect conformation with low energy for some protocols and some score functions, but not others. For 3 out of 7 targets in our comparison, including this one, most conformations that KIC (kinematic closure) with fragments samples, are close to the native structure. Again, for larger benchmarks, this is likely not as often the case.