CALCULATION METHOD OF BINDING FREE ENERGY, CALCULATION DEVICE OF BINDING FREE ENERGY, PROGRAM, SCREENING METHOD OF COMPOUND

摘要

A calculation method of binding free energy, which includes: calculating solvation energy (ΔG1) between a solvent and a compound; and calculating an energy change (ΔG2) between a bound state (λ=0) where the compound and a protein are bound, and an unbound state (λ=1) where the compound and the protein are not bound, wherein the calculating the energy change (ΔG2) includes: determining a distance (Dth), within which structure sampling is performed; calculating a change in binding energy (ΔG21) between the compound and the protein within a distance equal to or shorter than the distance (Dth), calculating a change in solvation energy (ΔG23) between the solvent and the compound with ignoring an influence of the protein, calculating a change in binding energy (ΔG22) between the compound and the protein with interpolation, and calculating a correction term (ΔG24) with respect to a standard state.

主权项

1. A calculation method of binding free energy between a compound and a protein in a solvent, the method comprising:
calculating solvation energy (ΔG1) between the solvent and the compound; and calculating an energy change (ΔG2) between a bound state (λ=0) where the compound and the protein are bound, and an unbound state (λ=1) where the compound and the protein are not bound, wherein the calculating the energy change (ΔG2) comprises: determining a distance (Dth), within which structure sampling is performed, based on a distance between the compound and the protein in the bound state (λ=0); calculating a change in binding energy (ΔG21) between the compound and the protein within a distance equal to or shorter than the distance (Dth) on a state (λ=λm) that is a state between the bound state (λ=0) and the unbound state (λ=1), the state (λ=λm) including a state in which a distance between the compound and the protein is equal to or shorter than the distance (Dth), calculating a change in solvation energy (ΔG23) between the solvent and the compound in the unbound state (λ=1) and a state (λ=λn) that can be regarded as the same to the unbound state (λ=1), with ignoring an influence of the protein, calculating a change in binding energy (ΔG22) between the compound and the protein on a state between the state (λ=λm) and the state (λ=λn), with interpolating from the state (λ=λm) and the state (λ=λn), and calculating a correction term (ΔG24) with respect to a standard state, based on a volume of a space calculated from the distance (Dth).