Ligands are supplied to DockM8 as an .sdf file. The ligand library is first standardized using the ChEMBLstructure-pipeline library, which uses RDKit to check, standardize and desalt ligands. Accurately predicting ligand protonation states remains a challenge in computational chemistry and few open-source libraries are available to perform this task . As a result, we used Gypsum-DL for both compound protonation and 3D conformation generation .