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Int. J. Mol. Sci. 2016, 17(5), 742; doi:10.3390/ijms17050742

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
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)
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Abstract

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
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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

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