Concepedia

Taming multiple binding poses in alchemical binding free energy prediction: the β-cyclodextrin host–guest SAMPL9 blinded challenge

Sheenam Khuttan, Solmaz Azimi, Joe Z. Wu, Sebastian Dick, Chuanjie Wu, Huafeng Xu, Emilio Gallicchio

Physical Chemistry Chemical Physics · 2023 · 17 citations · 42 references

DOIFull text

Open access

Concepts

Abstract

The binding free energies of the multiple binding poses of the βCD/phenothiazine host–guest complexes are integrated to form SAMPL9 predictions.

References

42

Automatic atom type and bond type perception in molecular mechanical calculations

Junmei Wang, Wei Wang, Peter A. Kollman et al. · Journal of Molecular Graphics and Modelling · 2006 · 5.6K citations

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GFN2-xTB—An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion Contributions

Christoph Bannwarth, Sebastian Ehlert, Stefan Grimme · Journal of Chemical Theory and Computation · 2019 · 4.2K citations · Full text

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Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

Alessandro Barducci, Giovanni Bussi, Michele Parrinello · Physical Review Letters · 2008 · 3.3K citations · Full text

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OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

Peter Eastman, Jason Swails, John D. Chodera et al. · PLoS Computational Biology · 2017 · 2.8K citations · Full text

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Epik: a software program for pK a prediction and protonation state generation for drug-like molecules

John C. Shelley, Anuradha Cholleti, Leah L. Frye et al. · Journal of Computer-Aided Molecular Design · 2007 · 2.1K citations

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