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As of March 22, 2011, there are 71,955 structures reported in RCSB Protein Data Bank (http://www.rcsb.org/pdb/home/home.do;jsessionid) and they are available to use for the scientific community , and the number of the reported macromolecules has been continuously increasing. On the other hand, free structure data bases, in which thousands of small molecules are accumulated and classified in terms of physico-chemical properties, have been made available in public. One of the notable examples is ZINC(http://zinc.docking.org/index.shtml). Based on these trends, we have been performing high-throughput virtual screening of small molecules against macromolecules such as protein tyrosine kinase, -glycosidase, -secretase, and cyclooxygenase, in order to aid in drug design and drug discovery.