Hi James, Since you got many answers in regards to visualization, I might offer some help on other end, namely the computations in SBDD. For this we have created ODDT https://github.com/oddt/oddt in my previous group, and it offers many protein ligand interaction and scoring functionality among many others. We have developed few novel ML scoring functions and protein-ligand extended connectivity fingerprints (PLEC FP). It is RDKit and openbabel based.
Together with my colleague Marta we also have created a bunch of functions to prepare the proteins in the RDKit named RDKit-fixer https://oddt.readthedocs.io/en/latest/rst/oddt.toolkits.extras.rdkit.html#module-oddt.toolkits.extras.rdkit.fixer In particular look into PreparePDBMol and PrepareComplexes functions. All of this functionality is template-based and assigns bond orders and protonation states based on the residue names, which is similar to other approaches. As a different solution there is PDBfixer https://github.com/pandegroup/pdbfixer based on OpenMM, although it was not performing well enough for our testcases, thus we've created aforementioned RDKit-fixer module in ODDT. See more ODDT publication: https://jcheminf.biomedcentral.com/articles/10.1186/s13321-015-0078-2 PLEC FP publication: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty757/5092926 PS. Desclaimer I'm the developer of ODDT, opinions are subjective ;) ---- Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl pon., 18 mar 2019 o 07:29 Malitha Kabir <malitha12...@gmail.com> napisał(a): > 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 >> > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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