Fig. 1: Key steps in the design workflow.
From: Complete computational design of high-efficiency Kemp elimination enzymes
a, KE of 5-nitrobenzisoxazole. ‘B’ is a base, implemented as the sidechain of Asp or Glu. b, Thousands of backbones are generated through combinatorial backbone assembly (step 1) and stabilized using PROSS29 (step 2, red spheres). Geometric matching43 and active-site (purple spheres) optimization with Rosetta yield millions of designs that are filtered by balancing energy terms that contribute to stability and activity (step 3). A few dozen top designs are chosen for further core (green spheres) and active-site stabilization (step 4). Following experimental screening (step 5), we apply FuncLib28 to the active sites of select functional designs (step 6). Illustrations in b (step 5) were created using BioRender (https://biorender.com).
