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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.

Fig 3

doi: https://doi.org/10.1371/journal.pcbi.1004335.g003