Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical (QM/MM) approach

By A. Cho, V. Guallar, B. Berne, Richard A. Friesner. Journal of Computational Chemistry, 2005

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Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock (2009, methodology): “One possibility is to consider the effect of the protein binding site on the ligand polarization using quantum chemical methods [19,20].”
Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. (2006, methodology): “39 We may incorporate this methodology into future XP Glide releases for optional use.”
Potential energy functions for protein design. (2007, background): “One possible compromise is to model key parts of the protein using quantum mechanics and the rest of the protein using molecular mechanics [40,41].”
Combining docking and molecular dynamic simulations in drug design (2006, background): “The mobility of both ligand and receptor, the effect of the protein environment on the charge distribution over the ligand, 37 and their interactions with the surrounding water molecules, further complicate the quantitative description of the process.”