Feature Request: Multiple-Ligand Simultaneous Docking to the Same Protein

[rjrich]

Thank you for creating DynamicBind. It is an excellent and useful software tool. However, I would like to make a feature request to make DynamicBind even more useful. Please consider enabling DynamicBind to dock two or more ligands simultaneously to the same protein. As you know, there are some proteins that can accomodate two ligands within the same catalytic or receptor site. Other scenarios include binding of a substrate or inhibitor to a protein that contains a cofactor as well as binding of a ligand to a catalytic or receptor site along with binding of another ligand to an allosteric modulatory site. Thank you for considering this enhancement of DynamicBind.

I tried first docking of a single ligand of the protposed pair of ligands to the protein, saving the complex, and using this complex as the receptor protein for the second ligand. During the inference, I used the option of putting the path to the protein in the ligand csv file and the option --no_clean. However, this did not work; the protein pdb file was cleaned anyway to remove the first ligand.