Macs in Chemistry

Insanely Great Science

Benchmark set for relative free energy calculations.

 

Free energy perturbation (FEP) is a method that is used in computational chemistry for computing free energy differences from molecular dynamics or Metropolis Monte Carlo simulations and used in a wide variety of applications.

FEP calculations have been used for studying host–guest binding energetics, pKa predictions, solvent effects on reactions, and enzymatic reactions. Other applications are the virtual Screening of ligands in drug Discovery, as well as for In silico mutagenesis studies. For the study of reactions it is often necessary to involve a quantum-mechanical (QM) representation of the reaction center because the molecular mechanics (MM) force fields used for FEP simulations can't handle breaking bonds.

In recent years this technique has gained popularity in predicting binding interactions in drug discovery, and it is great that Merck have made a benchmark dataset available on GitHub https://github.com/MCompChem/fep-benchmark. Details of which are described here DOI. Eight different targets are included together with 200 ligands.

CDK8, c-Met, Eg5, Hif2a, PFKFB3, SHP2, SYK, TNKS2


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