RDkit Discussion Group, RDkit has quite a number of useful tools and algorithms for ligand-based drug design (LBDD). However, what about structure-based drug design (SBDD)? Perhaps a few questions to motivate the discussion. 1) Since RDkit supposedly includes the force field MMFF, does this mean that one can read in reasonably prepared proteins (from a PDB file) and ligands(from a MOL file) and compute energies of the complex, proteins, and ligands and presumably interaction energies, etc? 2) Visualization is clearly important in SBDD. Has anyone developed a tool that nicely integrates macromolecular editing and visualization with RDkit? 3) Given the visualization capabilities of Jupyter, has anyone developed Jupyter/RDkit scripts for #1 and #2? I welcome thoughts and comments especially from those who have been thinking about or are wrestling with SBDD and RDkit integration. Thank you. Regards, Jim Metz
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