In Silico Screening for New Drug and Computational Chemistry

Toshikazu TAKADA

Fundamental and Environmental Research Laboratories, NEC Corporation
34, Miyukigaoka, Tsukuba 305-8501 Japan
Present address: Research Program for Computational Science, RIKEN
6th Fl., Meiji Seimei Kan, 2-1-1 Marunouchi Tokyo 100-0005 Japan

(Received: March 29, 2007; Accepted for publication: August 2, 2007; Published on Web: August 30, 2007)

A theoretical framework called QM/MM (Quantum Mechanics/Molecular Mechanics) is attracting considerable attention as a new approach to the handling of large scale bio-related molecules like proteins in membrane and solution. In the scheme, molecular regions of interest are described in quantum mechanical terms and the rest of the complex molecular system in classical manner, i.e., molecular mechanics. Since computational effort for the QM region increases roughly in proportion to the third power of the number of atoms, computational time is drastically decreased by choosing the QM space as small as possible. In this article, the basic concept of the QM/MM theory and a new attempt to overcome their problems in actual simulations are given. An application to new drug design is introduced, which has been developed in the BioGrid project organized by Osaka University and others.

Keywords: Quantum chemistry, QM/MM method, Molecular simulation, In Silico screening, Drug design

Abstract in Japanese

Text in Japanese

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