FIG. 1.

Flexible and mutable residues in a design for specificity. The apoptotic regulator CED4 forms two different dimers, one to block apoptosis (left; PDB id 2a5y [Yan et al., 2005]) and one to induce it (right; PDB id 3lqr [Qi et al., 2010]). We want to design for specificity (to block apoptosis), so we allow mutations to some residues in the binding site (blue). To accurately model the conformational changes induced by the mutations, we also model as flexible the residues on the opposite side of each interface that interact with the mutable residues (orange, pink). Analysis of this calculation and others is described in section 3.