Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity
Fig 3
Flowchart outlining the coupled moves method.
The protocol starts with an input structure of a protein–ligand interaction, and performs either coupled protein or ligand moves. Each protein move involves a backrub move coupled to side-chain repacking or design and each ligand move involves a rigid-body rotation and translation coupled to ligand repacking. A move is either accepted or rejected depending on the change in energy, and a total of N moves are performed, where N can be set by the user.