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A new computational method is developed for mapping of small ligand molecules on protein surfaces, which is in line with fragment-drug design, and this method has used three-dimensional reference interaction site model (3D-RISM) theory. The results have shown that some binding modes are affected by the ligand concentration.

CO escaping pathways of Myoglobin are examined in terms of three-dimensional (3D) distribution function that is calculated by the 3D-RISM theory. The partial molar volume changes through the CO escaping pathways have agreed with those from the experiment.

The ion binding by human lysozyme is examined in ionic solutions with the help of the three-dimensional (3D) RISM theory. The results have suggested that the theory could be applied to the selective transmission of ions by a channel protein.

This article focuses on a study according to which water molecules in a protein cavity were detected by a statistical-mechanical theory. Water molecules confined inside cavities in a protein are of great importance in understanding the structure, stability, and functions of the biomolecule. The simulation of such water molecules is as difficult as the protein folding itself. The study proves unambiguously that the common understanding was really a prejudice. It is interesting to compare the hydration structure obtained by the 3D-RISM theory with crystallographic water sites of X-ray structure.