Modified AutodockVina, OpenBabel, Convex-PL
We converted SMILES into 3d structures using OpenBabel. We paid particular attention to groups of ambiguous stereochemistry. When needed, we compared the stereochemistry with examples from the PDB and manually corrected the mismatches. We have collected homologous structures from PDB that bind similar ligands using PDB search with SMILES substrings.
We ran VINA with num_modes = 500, exhaustiveness = 1000, energy_range = 100. We clustered the solutions using symmetry-adapted RMSD of 0.4 A. This was computed using a patched version of LigAlign.