Hi James, As Paul mentioned about RDKit-3Dmol.js integration, I would like to share additional information. I wrote those scripts about 2 years ago and those do not have structure editing capabilities. I have plan to update those after June this year. Thank you.
Best regards, - malitha On Mon, Mar 18, 2019 at 1:39 PM Bakary N'tji Diallo <diallobaka...@gmail.com> wrote: > 2) For visualization nglview <https://github.com/arose/nglview>has lot > of capabilities. I run simulation on a cluster and with nglview in a > Notebook, the final trajectories can be directly be loaded in the notebook > for visualization. Here is a gallery of different usages for visualization > with nglview <http://nglviewer.org/ngl/gallery/index.html>. Loading > trajectories can be done through pytraj > <https://amber-md.github.io/pytraj/latest/_api/pytraj.all_actions.html> which > also has tone of analytical capabilities. It will be interesting to see to > see notebook with free energy calculation for protein-ligand systems, > especially including QM techniques. > > Le sam. 16 mars 2019 à 18:54, James T. Metz via Rdkit-discuss < > rdkit-discuss@lists.sourceforge.net> a écrit : > >> 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 >> >> >> >> >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > > > -- > > Bakary N’tji DIALLO > > PhD Student (Bioinformatics) <http://linkedin.com/in/bakarydiallo>, Research > Unit in Bioinformatics (RUBi) <https://rubi.ru.ac.za/> > > Mail: diallobaka...@gmail.com | Skype: diallobakary4 > > Tel: +27798233845 | +223 74 56 57 22 | +223 97 39 77 14 > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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