Re: [Rdkit-discuss] pharmacophore
On 30/03/2022 03:49, Patrick Walters wrote: One way to compare interactions (pharmacophores) in a binding site is to use interaction fingerprints. I've had a good experience with ProLIF. https://github.com/chemosim-lab/ProLIF Additionally, I know about all those open-source ones: - https://pharmit.csb.pitt.edu/ - https://github.com/gertthijs/pharao - https://github.com/DrrDom/pmapper On Tue, Mar 29, 2022 at 6:26 AM Muhammad Akram wrote: Hello Everybody, I am looking if there is a way to extract a pharmacophore from co-crystallized ligand using RDKit. Thank you so much in advance. Kind Regards, Mu ___ 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 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] pharmacophore
One way to compare interactions (pharmacophores) in a binding site is to use interaction fingerprints. I've had a good experience with ProLIF. https://github.com/chemosim-lab/ProLIF On Tue, Mar 29, 2022 at 6:26 AM Muhammad Akram wrote: > Hello Everybody, > > > > I am looking if there is a way to extract a pharmacophore from > co-crystallized ligand using RDKit. > > > > Thank you so much in advance. > > > > Kind Regards, > > Mu > ___ > 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
Re: [Rdkit-discuss] pharmacophore
Hi Mu, The RDKit has code for identifying pharmacophoric points and calculating the distances between them, but there is no pharmacophore perception tool in the core RDKit. Best regards, -greg On Tue, Mar 29, 2022 at 12:25 PM Muhammad Akram wrote: > Hello Everybody, > > > > I am looking if there is a way to extract a pharmacophore from > co-crystallized ligand using RDKit. > > > > Thank you so much in advance. > > > > Kind Regards, > > Mu > ___ > 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
[Rdkit-discuss] pharmacophore
Hello Everybody, I am looking if there is a way to extract a pharmacophore from co-crystallized ligand using RDKit. Thank you so much in advance. Kind Regards, Mu ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
