Rosetta FunFolDes – A general framework for the computational design of functional proteins
Fig 2
Benchmark test set to evaluate FunFolDes structural sampling.
A) Structural representation of the 14 targets used in the benchmark. In each target is highlighted the motif (red) and query (blue) regions, and the positions from which distance constraints were generated (light blue). Conformations of the motif and query regions, as found in the template structures, are shown superimposed in light grey. B) Full structure RMSD (Overall RMSD) and local RMSD for the query region (FunFolDes–Query Region) is presented for four targets (full dataset presented in S1 Fig). Overall RMSD compares results for the two simulation modes (FunFolDes Vs. constrained–ab initio (cst-ab initio)) and the two fragment generation methods (structure (blue) Vs. sequence-based fragments (green)) against their original target. FunFolDes more frequently samples RMSDs closer to the conformation of the target structure. Generally, structure-based fragments contribute to lower mean overall RMSDs. The FunFolDes–Query Region RMSD distributions show that the two fragment sets do not have a major importance in the structural recovery of the query region.