Fig 1. Design process for VEGF inhibiting D-protein with non-canonical amino acids.

A: schematic of the four sets of calculations performed in the thermodynamic integration step. Micro-canonical ensembles are generated for both wild type and mutated structures (ΔGmut) in bound and unbound states (ΔGassoc & ΔGdiss). Output energies are integrated using the equation shown to derive ΔG. See TI methods subsection. B: the four main design steps (MM = molecular model). C: complex ensemble generated by MD followed by clustering, representing the explored conformational space; D: interface residues identified for design in atomic resolution.