Inputting ligands as SDF files rather than SMILES

[rjrich]

Based on the example commands, it is not immediately obvious how to input ligands as SDF files rather than SMILES strings. For my initial test of DynamicBind, I used SMILES strings, and although I used RDKit to convert my SDF files to SMILES, DynamicBind rejected 9 out of 24 ligands. After figuring out how to input SDF files and running DynamicBind again, the program accepted all 24 ligands.

The developers of this excellent program might wish to add some explicit instructions or examples on how to use ligand formats other than SMILES. Accurate translation of 3D ligand files into SMILES can be problematic, especially with molecules that possess chiral P-atoms. In addition, compounds such as (R1)(R2)P=S can get converted to (R1)(R2)H-P-SH during conversion of SDF to SMILES or after other processing of ligands or protein-ligand complexes.

Thank you!