FIG. 3.

Speed: MARK* is up to 135 times faster than iMinDEE-A*-K*, and its speedups increase as iMinDEE-A*-K* takes longer. (A, B) Times to return the five best sequences for MARK* (blue, red) and iMinDEE-A*-K* (green) are shown. (A) Times for all 200 continuous design problems are shown, plotted against conformation space size. MARK* completes 15 challenging design problems (size larger than 10¹⁰ conformations, red triangles) that iMinDEE-A*-K* cannot. (B) Runtimes for the 185 designs completed by iMinDEE-A*-K*, sorted along the x-axis by iMinDEE-A*-K* runtime (ranks for designs given in Table 1 of the Supplementary Information in Jou et al., 2019), are shown. For all designs that required longer than 146 minutes, MARK* required less time (up to 135 times faster).