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. 2018 Jul 1;25(7):726–739. doi: 10.1089/cmb.2017.0267

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Copyright 2018, Mary Ann Liebert, Inc.

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FIG. 3. — BBK* is up to five orders of magnitude more efficient than iMinDEE//. BBK* completed all 204 designs within a 30-day limit, whereas iMinDEE// completed only 107. (A) The number of SS- bounds performed versus the number of sequences in the design space. Results are shown for computing only the best sequence (blue) and computing the best five sequences (orange). SS algorithms, including the best previous algorithm iMinDEE//, must compute binding affinity for all possible sequences (green curve). BBK* required up to 6 × 10⁵-fold fewer SS- bounds to find the best sequences. (B) The number of energy-minimized conformations by BBK* and iMinDEE// versus the number of sequences in the design space. iMinDEE// completed only 107 of 204 designs (left of the vertical line) before the 30-day timeout. For these designs, BBK* was up to 1700-fold more efficient. (C) BBK* and iMinDEE// running times versus the number of sequences in the design space. For the 107 designs completed by iMinDEE// within 30 days (left of the vertical line), BBK* was up to 800-fold more efficient than iMinDEE//.

Inline graphic — BBK* is up to five orders of magnitude more efficient than iMinDEE//. BBK* completed all 204 designs within a 30-day limit, whereas iMinDEE// completed only 107. (A) The number of SS- bounds performed versus the number of sequences in the design space. Results are shown for computing only the best sequence (blue) and computing the best five sequences (orange). SS algorithms, including the best previous algorithm iMinDEE//, must compute binding affinity for all possible sequences (green curve). BBK* required up to 6 × 10⁵-fold fewer SS- bounds to find the best sequences. (B) The number of energy-minimized conformations by BBK* and iMinDEE// versus the number of sequences in the design space. iMinDEE// completed only 107 of 204 designs (left of the vertical line) before the 30-day timeout. For these designs, BBK* was up to 1700-fold more efficient. (C) BBK* and iMinDEE// running times versus the number of sequences in the design space. For the 107 designs completed by iMinDEE// within 30 days (left of the vertical line), BBK* was up to 800-fold more efficient than iMinDEE//.