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Review

Recent Progress in Treating Protein–Ligand Interactions with Quantum-Mechanical Methods

Institute for Theoretical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89069 Ulm, Germany
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Author to whom correspondence should be addressed.
Academic Editor: Tatyana Karabencheva-Christova
Int. J. Mol. Sci. 2016, 17(5), 742; https://doi.org/10.3390/ijms17050742
Received: 16 March 2016 / Revised: 18 April 2016 / Accepted: 3 May 2016 / Published: 16 May 2016
(This article belongs to the Collection Proteins and Protein-Ligand Interactions)
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. View Full-Text
Keywords: protein/ligand interactions; quantum chemistry; density functional theory; semi-empirical quantum mechanical methods protein/ligand interactions; quantum chemistry; density functional theory; semi-empirical quantum mechanical methods
MDPI and ACS Style

Yilmazer, N.D.; Korth, M. Recent Progress in Treating Protein–Ligand Interactions with Quantum-Mechanical Methods. Int. J. Mol. Sci. 2016, 17, 742. https://doi.org/10.3390/ijms17050742

AMA Style

Yilmazer ND, Korth M. Recent Progress in Treating Protein–Ligand Interactions with Quantum-Mechanical Methods. International Journal of Molecular Sciences. 2016; 17(5):742. https://doi.org/10.3390/ijms17050742

Chicago/Turabian Style

Yilmazer, Nusret D., and Martin Korth. 2016. "Recent Progress in Treating Protein–Ligand Interactions with Quantum-Mechanical Methods" International Journal of Molecular Sciences 17, no. 5: 742. https://doi.org/10.3390/ijms17050742

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