タンパク質立体構造予測のための改良レプリカ交換法(応用,科学技術計算と数値解析,<特集>平成18年研究部会連合発表会)

概要

論文の詳細を見る
The native structure of protein corresponds to the global minimum of free energy. Replica-exchange method (REM) has been recently used to search the energy minimum in a huge conformation space of a protein. For large systems, however, applying REM can be costly since the number of replicas required for the conformation sampling increases. We have developed a variant REM called fragment REM (FREM), which is based on the existence of correlation between the local amino acid sequence and the local structure. Equilibrium distributions for poly-alanine were computed by the conventional MD, REM and the proposed FREM simulations. We have found that FREM successfully reduces the number of replicas needed for the simulation.
日本応用数理学会の論文
2006-09-25