Although RDKit is a widely used extremely versatile chemoinformatics software package, it still lacks efficient 3D molecule visualization capability. In this circumstance, 3Dmol.js is easy to use and an excellent molecule visualization library that works in web browser. Another important platform is jupyter that allows communication with python from web browser through notebook like interface. Jupyter has also made the codes easily readable with clean output by dint of markdown. So, keeping python as operational core engine that expectedly works as interface of RDKit while utilizing support from jupyter notebook and 3Dmol.js should be a very good combination to ensure high productivity in drug discovery settings. In this project, I would like to turn these combination to more viable solution by binding 3D molecule visualization (protein-ligand complex), ligand editing panel, conformer scrolling system, and channel for sending ligand from jupyter interface to force field that exists in RDKit for energy minimization. Needless to say, I would like to use openbabel for file format conversion and molecular data extraction system.



Malitha Humayun Kabir


  • Paul Czodrowski
  • Greg Landrum