Comparison of Rotamer Optimization Algorithms.

Fifteen rotamer optimization algorithms were compared by examining the energies they produced and their running times in a head-to-head comparison in optimizing rotamers for 10 K sequences. Details of the optimization algorithms are given in the Methods Section. We defined the “consensus energy” for each sequence examined as the lowest energy found by any of the algorithms. Each algorithm is described by the percentage of the trajectories where it reached the consensus energy, where it reached to within 0.001, to within 0.1, and to within 1 Rosetta energy units (REU) of the consensus energy, (in the columns labeled “% at Cons.”, “% w/i REU”, “% w/i REU”, and “% w/i 1 REU” respectively), the percentage of the trajectories for which it failed to find an energy within 100 REU of the consensus energy (labeled “% 100 REU), its mean running time, in seconds (labeled Time Avg.), and its relative mean running time as compared against the BMEC+sPR algorithm, which was the fastest (labled Rel. Perf.). Parenthetical percentages reflect these frequencies when considering only the subset of sequences with a consensus energy less than −30 REU. 8 K of the 10 K sequences fell into this category.