Algorithms and applications of QM/MM hybrid simulations for elucidation of functional mechanisms and structural-based rational design of biological molecules

18 November 2008 (Tue), 1:30 pm - 3:00 pm

4F seminar room, MANA Bldg., Namiki Site

Prof. Martin J. Field

Laboratoire de Dynamique Moleculaire, Institut de Biologie Structurale, France

Algorithms and applications of QM/MM hybrid simulations for elucidation of functional mechanisms and structural-based rational design of biological molecules

Interactions of biological macromolecules such as proteins, nucleic acids are the source of biological functions. However, it is difficult to perform theoretical investigations of such interactions based on their electronic structures, because of huge number of atoms and thermal fluctuations. To investigate these systems, quantum mechanics/molecular mechanics (QM/MM) calculations are utilized, in which the system is divided into QM and MM atoms. Here, QM regions correspond to active sites to be investigated, and are described on the basis of the quantum mechanics theory. MM regions correspond to the remainder of the system, and are described at the molecular mechanics level.

In this seminar, recent progresses in QM/MM hybrid calculations, in particular, of biological macromolecules, are presented, including pharmaceutical issues. Our original calculation methods and their applications into proteins and structure-based rational drug design of therapeutic regents on the basis of our original algorithms and systems for QM/MM hybrid simulations are also discussed.

Dr. Hiori Kino(木野日織）