Figure 4: A Python script that performs a very simple design in osprey 3.0.

The design searches over sequences in which residues A2 and/or A3 of the Atx1 metallochaperone protein (PDB ID: 1CC8)⁴⁷ are mutated; residues A2-A4 (i.e., residue 2-4 of chain A) are all modeled with sidechain flexibility, consisting of a discrete search over the Penultimate rotamer library⁴⁸’s rotamers for the specified amino acid types. The mutability, flexibility, and starting crystal structure are all specified in the “define a strand” section of the code. Advanced users can also modify the other sections to specify changes from the default search algorithms, energy function, and other modeling assumptions. This script uses the Max Product Linear Programming (MPLP) algorithm⁴⁹ to reduce the size of the A* search tree¹⁵ employed for sequence and conformational search without compromising accuracy; see Ref.²² for details.