(Received: April 5, 2007; Accepted for publication: May 10, 2007; Published on Web: June 29, 2007)
This review introduces the application of the Fragment molecular orbital (FMO) method. The ABINIT-MP and BioStation Viewer programs have been used for such applications. The FMO method was applied for problems of transcriptional regulation, including interactions of nuclear receptor, ligand, transcription factor, and DNA. Detailed interactions between biomolecules and the roles of each amino acid residue were revealed through analyses of inter-fragment interaction energy (IFIE), charge distribution, and orbital configuration. Electrostatic and van der Waals dispersion interactions were found to be equally important in molecular recognition. It was found that the inclusion of electron correlation was essential to obtain appropriate pictures. Other applications such as the photo-excitation process are also introduced.
Keywords: Fragment molecular orbital method, ABINIT-MP, BioStation Viewer, Bio-macromolecule, Molecular recognition, Nuclear receptor, DNA
Text in Japanese