Hydrogen bonds rebuilt by polarized protein-specific charges

► Three novel schemes on the basis of newly developed polarized protein-specific charge (PPC) have been proposed to perform protein structure refinement. ► The newly developed polarized protein-specific charge (PPC) can recover the broken H-bonds which are generated in the MD simulation on the basis of the conventional standard charge. ► This work is an implication for PPC's ability to refine experimental raw structures, such as NMR structure.