Watanabe T., Inadomi Y., Tanaka S., Nagashima U.
National Institute of Advanced Industrial and Science and Technology, JP
Keywords: DNA binding domain, estrogen receptor, fragment molecular orbital, zinc finger
The fragment molecular orbital (FMO) method was applied to evaluate the interaction between estrogen response element (ERE) in DNA and DNA binding domain (DBD) of estrogen receptor (ER). In order to calculate the whole electronic state of DNA-ERE and ER-DBD, we developed the SCC-DIIS method and the field scaling method. The SCC-DIIS method is for acceleration of the self-consistent charge (SCC) convergence, and the field scaling method changes the field effect from other fragments for stable convergence. Hybridization of these two methods made it possible to calculate the whole electronic state of DNA-ERE and ER-DBD.
Journal: TechConnect Briefs
Volume: 1, Technical Proceedings of the 2004 NSTI Nanotechnology Conference and Trade Show, Volume 1
Published: March 7, 2004
Pages: 176 - 179
Industry sector: Medical & Biotech
Topics: Biomaterials, Informatics, Modeling & Simulation
ISBN: 0-9728422-7-6