Figure 1.

Sampling of binding modes for the pairs GUA–TYR (4 Å) and URA–TRP (4 Å) in water as well as GUA–ASP (5 Å) and GUA–GLU (6 Å) in methanol at a restraining distance r₀ corresponding to a PMF minimum. Centers of the most populated cluster are shown in an opaque stick representation, while snapshots of sidechain analogs output every 200 ps are shown in a transparent stick representation. Percentages represent fraction of time that stacking interactions (TYR or TRP) or hydrogen bonds (ASP and GLU) are present.