HydraMap v1.0

A tool to predict potential water molecules in the protein binding pocket

Example 1 predict the locations and energies of water molecules in the binding site of FXa. The protein structure is from the complex with PDB entry 1EZQ. The bound ligand in the crystal structure is used to define the binding site.

Command:
./wsitem 1ezq_protein.pdb 1ezq_ligand.mol2 apo 4.0 5.0 2.0 10
Default parameter files: PARA_PRO.TXT, PARA_WAT.TXT
Generated files:

(a) wsite.pdb
A PDB file with three coordinates of all predicted water molecules.

Figure 3. The locations of predicted water molecules (cyan) in the protein FXa (PDB code: 1EZQ)

(b) wsite.log:

Each line represents a hydration site.
Column 3, 4 and 5 list the coordinates of the water molecule.
Column 6 gives the predicted PMF energy of the water molecule.

(c) grid.txt

Each line represents a grid point.
Column 2, 3 and 4 list the coordinates of a grid point.
Column 5 gives the PMF energy of the grid point.

Example 2 Compare the water molecules predicted by HydraMap and WATsite.

Command:
./getwat 1ezq_protein.pdb 1ezq_ligand.mol2 wsite.pdb 4.0
Rename the generated file "wat.pdb" to "ws_4A.pdb".

./getwat 1ezq_protein.pdb 1ezq_ligand.mol2 1ezq_md.pdb 4.0
Rename the generated file "wat.pdb" to "md_4A.pdb".

Command:
./analws 1ezq_ligand.mol2 ws_4A.pdb md_4A.pdb 4.0

Output:

Figure 4. Comparisons of the water molecules predicted by HydraMap (green) and WATsite (red) within 4Å of the protein and ligand atoms.

Example 3 calculate the PMF energies of predicted water molecules with the consideration of the contributions from water-water interactions.

Command:
./dG wsite.pdb grid.txt
The generate file "wsite.log" is similar to the one predicted by "wsitem".

The last column lists the PMF energy of the water molecule by considering the water-water interactions.