Figure 2.

(a) Site-specific contact ratio of WW domain, where the contact ratio of a residue was obtained by counting the number of frames of the residue in contact with Gd@C₈₂(OH)₂₂ over all time frames; (b) Residues involved in contact with Gd@C₈₂(OH)₂₂; (c) The binding free energy surface, where D_KM is the minimum distance between Gd@C₈₂(OH)₂₂ and the signature residues (Y28 and W39) of the WW domain and S_PM is the contacting surface area; and (d) Representative binding modes found in the global minimum. Yellow: key residues, white: hydrophobic, green: non-charged polar, red: negatively charged and blue: positively charged residues.