I'd also be interested in Juptyer notebooks for this. Thanks Tyler!
Curt
On Tue, Nov 28, 2017 at 8:26 AM, Tyler Backman <tback...@lbl.gov> wrote:
> Hi Jim,
>
> MiBIG is a useful database of natural product gene clusters and
> structures, which you can download in JSON format here, and use pretty
> easily from within Python:
> https://mibig.secondarymetabolites.org/repository.html This also
> includes pathway and organism information.
>
> Secondly, our ClusterCAD database is built with RDKit and Django, but
> only includes Type I modular PKSs imported from MiBIG. You can use it
> online at clustercad.jbei.org, or view the code and launch a docker
> install locally from https://github.com/JBEI/clusterCAD. Internally,
> it has a RDKit postgresql database, and includes predicted chemical
> intermediates at each step of biosynthesis in addition to final
> products. It is hand curated, to improve on the automatic AntiSMASH
> annotations in MiBIG. I will gradually expand this to support a
> greater diversity of natural products. I could send you an example
> Jupyter notebook for using it programatically.
>
> Sincerely,
> Tyler
>
> On Mon, Nov 27, 2017 at 1:30 PM, James T. Metz via Rdkit-discuss
> <rdkit-discuss@lists.sourceforge.net> wrote:
> > RDkit Discussion Group,
> >
> > My apologies in advance if my request is not appropriate for this
> > discussion group.
> >
> > Given a small molecule that might have some resemblance to natural
> > products,
> > can someone suggest a free, comprehensive, PYTHON/RDkit searchable
> database
> > of natural products that might be suitable for similarity and
> substructure
> > searching.
> >
> > I am aware of a few websites that permit searching on the website. If
> > possible,
> > I would like to programmatically search by running a PYTHON/RDkit script
> on
> > my
> > local machine and then return the structures of related molecules to my
> > local script.
> >
> > I would prefer not having to download and store a huge database.
> >
> > Also, if possible, it would be important to return the organism(s)
> that
> > creates
> > the natural product. Pathway information would be also very, very
> helpful.
> >
> > I greatly welcome comments and suggestions.
> >
> > Thank you.
> >
> > Regards,
> > Jim Metz
> > Northwestern University
> >
> >
> >
> >
> >
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>
>
>
> --
> Tyler W. H. Backman
> Postdoctoral Fellow
> Lawrence Berkeley National Laboratory
> Joint BioEnergy Institute
>
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