Alchemical approach performance in calculating the ligand-binding free energy
Sơn Tùng Ngô, Quynh Mai Thai, Trung Hai Nguyen, Nguyen Ngoc Tuan, T. Ngoc Han Pham, Hường Thị Thu Phùng, Dương Tuấn Quang · RSC Advances · 2024
free energy perturbation (FEP) simulations is overestimated over the experimental value. Particularly, the electrostatic interaction free energy rules the binding process of ligands to AmpC and GluK1. However, the van der Waals (vdW) interaction free energy plays an important role in the ligand-binding processes of HSP90 and SARS-CoV-2 Mpro. The obtained results associate with the hydrophilic or hydrophobic properties of the ligands. This observation may enhance computer-aided drug design.