New Publication on Winning the 2018 D3R Grand Challenge 4

In the framework of the 2018 Drug Design Data Resource (D3R) grand challenge 4, blinded predictions on relative binding free energy were performed for a set of 39 ligands of the Cathepsin S. We leveraged the GPU-accelerated thermodynamic integration (GTI) of Amber 18 to advance our computational prediction. We outperformed all other participants in this session. The success in a blinded prediction strongly suggests that alchemical free energy calculation in Amber is a promising tool for future commercial drug design.

Blinded prediction of protein–ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4. Zou, J., Tian, C. & Simmerling, C. J Comput Aided Mol Des 33, 1021–1029 (2019).