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Introduction to QM/MM Simulations

Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have become a popular tool for investigating chemical reactions in condensed phases. In QM/MM methods, the region of the system in which the chemical process takes place

QM and QM/MM Simulations of Proteins

optimization and dynamic simulations of peptides and proteins. In this chapter, we introduce methodological developments such as the QM/MM framework and linear-scaling QM that make efficient calculations on large biomolecules possible. We identify

MM-GB/SA Rescoring of Docking Poses

binding modes, but struggle when predicting the corresponding binding affinities. The rescoring of docking poses using the MM-GB/SA technique has emerged as an important computational approach in structure-based lead optimization as it provides