Water in protein cavities: A procedure to identify internal water and exchange pathways and application to fatty acid-binding protein

A computational approach based on Delaunay triangulation is presented to identify internal water molecules in proteins and to capture pathways of exchange with the bulk. The implemented procedure is computationally efficient and can easily be applied to long molecular dynamics trajectories of protein simulations. In an application to fatty acid-binding protein in apo-form and with bound palmitate, several protein orifices known from crystal structures have been confirmed to be major portals of solvent exchange. Differences between the two forms of the protein are observed and discussed.