Dear James, Ad 1) Paolo Tosco did an integration of openMM and also was able to run a MD within Jupyter (partly covering (3)). Here is a link: https://github.com/rdkit/UGM_2017/blob/master/Presentations/Tosco_RDKit_OpenMM_integration.pdf
Ad 2) About 5 years ago, James Davidson presented at the RDKit UGM a very neat editing integration within PyMOL. However, to the best of my knowledge, there is no code availabl. Ad 3) As part of GoogleSummerOfCode, Malitha Kabir worked on the RDKit/3dmol.js integration which was also released to the stable RDKit branch. https://github.com/malithakabir/RDKitGSoC2017 I would love to see more SBDD integration of the RDKit especially together with Jupyter notebooks. In my case, I would then use this code basis for teaching SBDD on the basis of RDKit/Jupyter. Sooner or later, I might find a student working on this topic, but I cannot give you a clear timeline. Best regards, Paul (www.czodrowskilab.org<http://www.czodrowskilab.org>) Von: "James T. Metz via Rdkit-discuss" <rdkit-discuss@lists.sourceforge.net> Antworten an: "James T. Metz" <jamestm...@aol.com> Datum: Samstag, 16. März 2019 um 17:54 An: "rdkit-discuss@lists.sourceforge.net" <rdkit-discuss@lists.sourceforge.net>, "jamestm...@aol.com" <jamestm...@aol.com> Betreff: [Rdkit-discuss] Structure-Based Drug Design 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 Wichtiger Hinweis: Die Information in dieser E-Mail ist vertraulich. Sie ist ausschließlich für den Adressaten bestimmt. Sollten Sie nicht der für diese E-Mail bestimmte Adressat sein, unterrichten Sie bitte den Absender und vernichten Sie diese Mail. Vielen Dank. Unbeschadet der Korrespondenz per E-Mail, sind unsere Erklärungen ausschließlich final rechtsverbindlich, wenn sie in herkömmlicher Schriftform (mit eigenhändiger Unterschrift) oder durch Übermittlung eines solchen Schriftstücks per Telefax erfolgen. Important note: The information included in this e-mail is confidential. It is solely intended for the recipient. If you are not the intended recipient of this e-mail please contact the sender and delete this message. Thank you. Without prejudice of e-mail correspondence, our statements are only legally binding when they are made in the conventional written form (with personal signature) or when such documents are sent by fax.
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