Table 4 Absolute protein-ligand binding free-energy perturbation calculations

From: Prospective de novo drug design with deep interactome learning

ChEMBL ID

ΔG / kcal ⋅ mol−1

pEC50

Compound 1

-20.1

5.83

Compound 2

-19.7

5.64

ChEMBL391987

-22.3

6.94

ChEMBL241299

-18.4

6.51

ChEMBL213355

-19.1

6.82

ChEMBL212591

-19.7

6.64

  1. The numbers represent the calculated absolute protein-ligand binding free-energy perturbation (ABFEP, ΔG) for compounds 1 and 2, and ligands from the ChEMBL database with known sub-micromolar PPARγ activity (database entries ChEMBL391987, ChEMBL241299, ChEMBL213355, ChEMBL212591). The ABFEP calculations were executed with default parameters over a simulation period of 5 ns. (see Methods).
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