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. Author manuscript; available in PMC: 2022 Jun 1.
Published in final edited form as: Curr Opin Struct Biol. 2021 Feb 24;68:194–207. doi: 10.1016/j.sbi.2021.01.007

Fig 4.

Fig 4.

A protocol for evolution-based protein-protein interaction design used by EvoDesign. The procedure starts from an input complex, for which monomer/interface structural homologs are identified from the PDB library through TM-align and iAlign searches, respectively. Structural profiles are then constructed from the alignments of the monomer/interface analogs and used in conjunction with a physics-based potential, EvoEF2, to guide the REMC simulations to design novel protein sequences. The final designs are selected from the center of the largest cluster of designed sequence decoys.