Computation and properties of atomic charges based on the penalized regression model in proteins

Abstract

In the molecular dynamics simulation of protein, the RESP charge determined for each residue is used as the atomic charge. We have concluded that more reasonable atomic charges including the interaction in protein conformation were obtained by using the result of canonical molecular orbital calculation in the whole protein. In this study, by the penalized regression method, such as the Ridge regression and Lasso regression, the charges of the buried atom were mathematically evaluated.