Anna Cooper

Thanks, a tutorial from the web was used for my workflow: prepare protein and ligand, define the binding site, and finally dock. But that directly converts receptor(.pdb) file to pdbqt file without separating them, and I also find a few amino acid residues are lost in this progress, does that matter in the final results?

Thanks, a tutorial from the web was used for my workflow: prepare protein and ligand, define the binding site, and finally dock. But that directly converts receptor(.pdb) file to pdbqt file without separating them, does it matter the final results?

Hello! I am a novice in molecular docking and have some confusion. Why is the receptor.pdbqt file(that downloads from PDB then removes ligands and charges by autodock) prepared for docking, different from the receptor.pdbqt obtained from (python) smina processing? Many Thanks!

Thanks! However, does it means that smina can't convert binding affinity to dissociation constant using formula as following: Ki =Kd = exp(δG/(R * T))

What's the default temperature when running smina dockings?

Hi, how to put Boron related changes in smina when I use Jupyter virtual environment?