Green Solvents app: complete facelift
Posted by Dr. Alex M. Clark in cheminformatics, green solvents, iOS, mobile devices, Uncategorized on 20-Sep-2016
Way back when, I threw together an app called Green Solvents, which got started anachronistically from a tweet by Sean Ekins (which I misinterpreted, but it got the conversation started, so all is well). Since mid-2011, the app hasn’t had much attention, but that has now changed: it has been rewritten and given a much more modern look. The overhauled version is live on the iTunes AppStore, and is free to anyone with an iThing. Read the rest of this entry »
BioAssay Express: downloading SAR datasets
Posted by Dr. Alex M. Clark in bioassays, cheminformatics, public databases, XMDS on 28-Aug-2016
The last post described the addition of molecules to the BioAssay Express project, and alluded to the near term intention of making this actually useful for something. The first round of utility is now in place: the ability to select columns and download the molecules as a single SDfile, suitable for use as a structure-activity dataset. Read the rest of this entry »
BioAssay Express: now with molecules
Posted by Dr. Alex M. Clark in bioassays, Uncategorized on 25-Aug-2016
In the previous post, I introduced the BioAssay Express project, which is based on the idea that when assay protocols are described using semantic annotations rather than just scientific text, a whole realm of software analysis becomes possible. Whenever there’s a bioassay experiment protocol at hand, chances are there are also some molecules with activity measurements not far away: which is the subject of this article. Read the rest of this entry »
BioAssay Express (a bit of an unveil)
Posted by Dr. Alex M. Clark in bioassays, Uncategorized on 3-Aug-2016
It’s time to start writing about the BioAssay Express project, since it has been technically developed out in the open. This is what has been taking up the majority of my time for the last half year or so, and it has the potential to make an important contribution to the drug discovery process. Read the rest of this entry »
An overdue status update
Posted by Dr. Alex M. Clark in Uncategorized on 2-Aug-2016
It’s been awhile since I posted, but this welcome gift shown to the right reminded me to do so: one of the outputs from the honeycomb clustering algorithm is featured on the Journal of Chemical Information and Modeling cover page, for an article driven by Sean Ekins. My main contribution was the diagram technique, which hadn’t been described in the literature before, but has been demonstrated within the Approved Drugs and PolyPharma apps.
What I have been actively working on these last couple months has involved another sabbatical at the Collaborative Drug Discovery mothership in the San Francisco Bay Area, helping out with a number of R&D projects, but most significantly the BioAssay Express. This is a project you will be hearing about more in the near future: it has been somewhat on the down-low so far, despite being implemented in the open, with the entire project being deployed to a public internet-facing website with no security of any sort. It’s all about describing bioassay protocols using well structured terminology, rather than the rather retro best practice of writing everything down in scientific English jargon. Stay tuned for more.
Reaction similarity searching with MolSync
Posted by Dr. Alex M. Clark in chemical reactions, cheminformatics, chemspider on 31-May-2016
To continue on in the series of reaction-based cheminformatics on the MolSync website, the final missing search piece has now been implemented: reaction similarity. This works in a manner that is analogous to the transform feature, insofar as if you just draw one side of the reaction, or draw both sides but provide no atom-to-atom mapping information, the search behaviour just uses the molecules as-is. If you do provide atom mapping, though, the search gets a whole lot more specific. Read the rest of this entry »
MolSync reaction searching: atom mapping
Posted by Dr. Alex M. Clark in chemical reactions, cheminformatics, cloud-servers on 29-May-2016
The latest unit of progress for the molsync.com site is the addition of an interface for atom mapping. As mentioned in the previous post, basic reaction searching capabilities are operational, but more sophisticated techniques require a way to specify which atoms map to each other on each side of the reaction scheme, in order to describe a transformation. Read the rest of this entry »
