Efficient and Accurate Hydration Site Profiling for Enclosed Binding Sites.

ABSTRACT

Molecular dynamics (MD) simulations allow for accurate prediction of the thermodynamic profile of binding-site water molecules critical for protein-ligand association. Whereas this hydration-site profiling converges rapidly for solvent-exposed sites independent of the initial water placement, an accurate and reliable placement is required for water molecules in occluded binding sites. Here, we present an accurate and efficient hydration-site prediction method for occluded binding sites combining water placement based on 3D-RISM and MD simulations using WATsite.