Fig. 5

This workflow demonstrates the final stage of refinement for PDB structures, performed to replace atomic coordinates of atoms in a mutated residue with atomic coordinates corresponding to the wild-type residue. Using a combination of Biopython modules and the AMBER suite of programs, each PDB structure is modified and the final structure is minimized. For example, an original crystal structure and its wild-type sequence differ by two residues (Glu115His and Glu131Gln). The modified structure is reverted back to the original wild-type sequence in three stages: (i) all atoms in the R-group of the target amino acid (except for the peptide backbone atoms) are stripped from the file; (ii) new atoms with their respective 3D atomic coordinates are placed in the “empty” amino acid ‘site’ (e.g., the R-group atoms of Glu); (iii) the modified structure undergoes energy minimization using a steepest descent algorithm to relieve any bad contacts (i.e., steric hindrance) that may be caused by the addition of new atoms