HyPred predicts the density of solvent in the hydration layer around proteins.
Given the hydration shell density crystallographic water sites can be
predicted. A web server for doing HyPred calculations can be found
A detailed description of HyPred can be found in . A summary of HyPred can be found below.
Protein atoms are grouped into classes using two different categorizations of atom types. One specification collects heavy atoms into groups according to their element type (e.g., C, N, O, S...), while hydrogen atoms are grouped together depending on the atom to which they are bonded (e.g., CH, NH, OH...). The other more detailed specification defines the atom groups according to both their elemental character and amino acid type. The more detailed set assigns each unique atom in each amino acid type as an atom type. The detailed set provides one source of improvement over Pettitt who classifies atoms only according to the element. When cubes are equidistant from atoms of the same type, the densities of the cubes are averaged. This gives the pRDFs. Sample pRDFs are shown in figure 1 d.
The reconstruction of the hydration shell density without additional MD simulations begins with the protein in the absence of water. The protein and surroundings are partitioned into a grid of cubes as in the mean-field approach of the previous subsection. Let r designate the distance between the center of cube i and the closest scaled van der Waals surface, say of atom type A. Each cube i outside of the protein is assigned the density gA(r) from the pRDF for the given protein atom type A, the separation r, and the atom type closest to the cube's center. The scale factor (0.53) is optimized by minimizing the sum of the R factors of the three proteins. Densities in cavities are set to zero. A sample prediction for ubiquitin is illustrated in figure 1 g. Figure 1 b shows the average density from the MD simulation.
 Virtanen, Jouko, Makowski, Lee, Sosnick, Tobin R., & Freed, Karl F. (2010) Modeling the hydration layer around proteins: HyPred Biophysical Journal 99:1611-1619
 Makarov, VA Andrews, BK & Pettitt, BM (1998) Reconstructing the protein-water interface Biopolymers 45:469-78