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
