Recent progress in treating protein–ligand interactions with quantum-mechanical methods

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Abstract

© 2016 by the authors; licensee MDPI, Basel, Switzerland. We review the first successes and failures of a “new wave” of quantum chemistry-based approaches to the treatment of protein/ligand interactions. These approaches share the use of “enhanced”, dispersion (D), and/or hydrogen-bond (H) corrected density functional theory (DFT) or semi-empirical quantum mechanical (SQM) methods, in combination with ensemble weighting techniques of some form to capture entropic effects. Benchmark and model system calculations in comparison to high-level theoretical as well as experimental references have shown that both DFT-D (dispersion-corrected density functional theory) and SQM-DH (dispersion and hydrogen bond-corrected semi-empirical quantum mechanical) perform much more accurately than older DFT and SQM approaches and also standard docking methods. In addition, DFT-D might soon become and SQM-DH already is fast enough to compute a large number of binding modes of comparably large protein/ligand complexes, thus allowing for a more accurate assessment of entropic effects.

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Yilmazer, N. D., & Korth, M. (2016, May 1). Recent progress in treating protein–ligand interactions with quantum-mechanical methods. International Journal of Molecular Sciences. MDPI AG. https://doi.org/10.3390/ijms17050742

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