Format

Send to

Choose Destination
Int J Mol Sci. 2016 May 16;17(5). pii: E742. doi: 10.3390/ijms17050742.

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

Author information

1
Institute for Theoretical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89069 Ulm, Germany. duygu.yilmazer@uni-ulm.de.
2
Institute for Theoretical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89069 Ulm, Germany. martin.korth@uni-ulm.de.

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.

KEYWORDS:

density functional theory; protein/ligand interactions; quantum chemistry; semi-empirical quantum mechanical methods

PMID:
27196893
PMCID:
PMC4881564
DOI:
10.3390/ijms17050742
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Multidisciplinary Digital Publishing Institute (MDPI) Icon for PubMed Central
Loading ...
Support Center