PredHydSite v1.0

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

What is PredHydSite?
PredHydSite is used to predict potential water molecules in the protein binding pocket. It contains two modules, wsite and wsiteGen. The former uses the bound ligand to set the grid box in the binding pocket. It can used to predict water molecules in the pocket, with or without the ligand. The latter uses a known point (x, y, z) or a bound ligand to set the grid box around the binding pocket.

Readme File for PredHydSite

This package is used to piredict potential water molecules in the protein binding pocket. It contains two modules, wsite and wsiteGen. The former uses the bound ligand to set the grid box in the binding pocket. It can used to predict water molecules in the pocket, with or without the ligand. The latter uses a known point (x, y, z) to set the grid box around the binding pocket. 

1. Please decompress the file PredHydSite.tar.gz
   tar xvfz PredHydSite.tar.gz

2. Compile the program by running the file "compile.sh"
   ./compile.sh

3. Usage:
   wsite
   ./wsite protein_file ligand_file apo/holo [ D=3.0 cut=0.0 c_rep=1.50]
   protein_file: PDB format;
   ligand_file: Mol2 format, used for defining the protein binding pocket;
   apo/holo: determine whether the ligand is included in the prediction of water locations;
   D: the grid box is D angstrom away from the boundaries of the ligand, default 3.0A;
   cut: cutoff value for defining favorable PMF values in water site clustering, default 0.0;
   c_rep: distance cutoff value for defining protein atoms replaced by water molecules, default 1.50A.

   Three default parameter files are required including:
   PARA_PRO.TXT: PMF parameters for protein atom and water molecule;
   PARA_WAT.TXT: PMF parameters between water molecules, used for calculating interactions between water molecules;
   PARA_LIG.TXT: PMF parameters for ligand atom and water molecule, only required if the "holo" state is assigned.
   After running the command, a log file "wsite.log" and a PDB file "wsite.pdb" are generated. 

   wsiteGen
   ./wsiteGen protein_file x y z a b c cut=0.0 c_rep 
   protein_file: PDB format;
   x, y, z: define the center of the grid box;
   a, b, c: the length, width and height of the grid box
   cut: cutoff value for defining favorable PMF values in water site clustering, default 0.0;
   c_rep: distance cutoff value for defining protein atoms replaced by water molecules, default 1.50A.
   PARA_PRO.TXT and PARA_WAT.TXT are default parameters.
   Note: this program is only used to predict water locations and energies for an apo protein.
	


Obtain the PredHydSite v1.0 software suite
The PredHydSite2 software suite is now freely available for academic users. The PredHydSite suite includes the source codes and executable codes (for Linux platforms) of all major functions, the user manual, and the necessary material for running the several demo examples described in our publication. It is provided as a [TAR.gz package] (2.4 MB in size).

Reference:
  1. Yan Li, and Renxiao Wang*, "PredHydSite v1: ", Journal of XXXX, 2017, in revision


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