Publication： Journal of Chemical Physics

Date of Publication: 06 October 2009

Authors： Art E. Cho, Jae Yoon Chung, Minsup Kim, and Kichul Park

DOI: https://doi.org/10.1063/1.3239504

We develop a docking protocol based on quantum mechanical/molecular mechanical calculations in which quantum mechanical energy is used as scoring. We test the protocol with three groups of examples with various binding site characteristics. The new docking method performs as well as or better than conventional docking methods in all three groups. In particular, for proteins with primarily hydrophobic binding sites, structural motifs with possible π-π interactions are often found and it is shown that these can be better modeled with quantum mechanical scoring docking than force field based methods. It seems that the new method performs in such cases to a great accuracy.