Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations

• DOI: 10.1021/acs.jpcb.1c01862
• Publication Date: 2021-04-29T16:49:01Z
• Authors: Kiyoshi Yagi; Shingo Ito; Yuji Sugita
• Keywords: QM/MM; Interface (matter)

Understanding molecular mechanisms of enzymatic reactions is vital importance in biochemistry and biophysics. Here, we introduce new functions hybrid quantum mechanical/molecular mechanical (QM/MM) calculations the GENESIS program to compute minimum-energy pathways (MEPs) free-energy profiles reactions. For this purpose, an interface developed utilize a highly parallel electronic structure program, QSimulate-QM (https://qsimulate.com), calling it as shared library from GENESIS. Second, algorithms search MEP are implemented, combining string method (E et al.