1)Molecular surface of the protein molecule is first evaluated.
2)Molecular surface are just points on the surface of the protein represented by x, y and z coordinates.
3)Points on the molecular surface can be classified into two types namely the contact points, reentrant points.
4)By comparing the x y z and x’, y’, z’ coordinates the direction to place the dummy water molecule is determined.
5)Check for the steric clashes between dummy water molecule and other atoms of the protein molecule.
6)In case of steric clash, adjust the coordinates of dummy water molecule to slightly alter the position.
7)The above procedure is repeated to pack water molecules from the protein’s molecular surface upto a 3 Angstrom threshold.
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