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Recent progress of molecular biology revealed a large amount of information related to the structures and functions of genes and proteins. The information was deposited in databases such as that of National Center for Biotechnology Information (NCBI) supported by National Institute of Health, USA. Most of information are free to access, and are very valuable asset not only to the researchers in biology field, but also to the teachers and students studying biology. In this study, we have developed two one-hour instruction modules related with the concepts of enzyme structure and function for the intensive biology course in high school. In order to make the best use of the information in NCBI web site, we used Molecular Modeling Database to show and manipulate the three-dimensional structure of active site, enzyme-substrate complex, and the differences between pro- enzymes (zymogens) and activated enzymes. The protein database and BLAST program were also used to display the differences between pro-enzyme and activated enzyme. When we applied these modules to the 37 students of girls' high school located in Seoul, most of students showed no difficulties to manipulate the NCBI databases following the instructions, and the students' understanding of major concepts such as the active site, the inhibitor, and zymogen activation were remarkably improved after these two classes. Also, most of students showed great interest in surfing NCBI web site to look for biotechnology information. Based on this study, the use of NCBI databases for the high school intensive selective courses appeared to be an attractive way to inspire the student to study biology and to improve the students’ understanding of biological concepts.