It seemed appropriate to include a new topic to the Open Drug Discovery Teams project: Lyme Disease. After a road trip through New England this summer, seeing signs everywhere warning visitors to be ultra careful not to do anything reckless such as walking anywhere near green foliage, then reading articles about how the disease is actually an underdiagnosed epidemic, it might be time to start thinking of it in the same terms as neglected tropical diseases.
As a continuation of the previous post about generating scaffolding schemes to help search for new tuberculosis drugs, the next step is to pose the question: what about known compounds that fit into the structure-activity scheme, but haven’t been tested for activity against TB? As it happens, this question can be answered by scripting in some preexisting functionality. Continue reading
One of the projects that has been keeping me busy lately is a structure data-mining exercise intended to reveal some interesting scaffold hypotheses that can contribute to research into finding new cures for tuberculosis. The process is at an early stage, but if you’re interested in taking a look at some of the preliminary results, you can view them here. Continue reading
The Living Molecules app has been out for awhile now, and in a few days I’m going to embark on a road trip Rhode Island to participate in a Gordon Conference about visualisation in scientific education. I’ll be bringing with me a poster that describes the virtues of using the Living Molecules app to create molecular glyphs to embed in posters. These glyphs function like QR codes, except that instead of embedding generic data (usually a URL), they encode a way for the reader to lookup chemical data, which can be downloaded and displayed. There’s a reason for the name of the app, other than having a bit of a ring to it. Continue reading
If not, then you need to get out your iPhone/iPad (or borrow someone else’s), make sure you have the Living Molecules app installed, and capture the glyph to find out.
Further to the previous post that mentioned a new atom-mapping interface for the Mobile Molecular DataSheet (MMDS) app, the next step is an atom-to-atom pairing interface for reactions. A very short 30 second YouTube clip will show you how this works. Continue reading
The next version of the Mobile Molecular DataSheet is going to add a couple of user interface segments for viewing and editing the atom mapping number property. Shown on the right is the menu bank for providing mapping numbers for an individual molecule. Perhaps not so very interesting in and of itself, but the next step is to construct a slightly more intricate user interface for providing atom-to-atom mapping pairs for reactions.
In case you’re wondering, the answer is yes: this is going somewhere specific. Atom-to-atom mapping is a core prerequisite for getting into the world of reaction transforms.
The latest version of SketchEl (1.60) has added a new feature: sharing of content via molsync.com. From either the molecule editor or the datasheet editor, the underlying content can be directly uploaded, making it openly accessible to the greater internet.
While SketchEl is not technically a product of Molecular Materials Informatics, the copyright is held by me, it’s made available via the Gnu Public License, and it gets a bit of maintenance from time to time. It is a conventional and fairly capable 2D structure drawing program that is written in pure Java, and runs on all the major platforms. It can even be used as an applet, though that doesn’t matter as much as it used to. It also allows editing of molecular spreadsheets (“datasheets”) that contain molecules and various scalar data. Over the years (since 2005) it has served as a test bed for a few ideas, like the SketchEl molecule file format, and I still use it regularly for editing structures and collections.
The newly added sharing feature offers to upload the current molecule or datasheet. Once the upload is complete, the result is available in the form of a URL, which can be opened in the browser, e.g. http://molsync.com/share?mol=3161:
This is the same workflow that is available via several mobile apps, like MMDS and MolPrime+, either for sharing directly as a web page, or as a prelude to tweeting out the data. Once you have the data uploaded to the site, the content is served up in viewable form, and can be downloaded in various cheminformatics and graphics formats. It can be shared by any sort of internet distribution means, and there are lots of clickable icons for bouncing it out via Twitter, Facebook, LinkedIn, Google+, etc.
Notice also that the page includes the molecular recognition glyph – that’s the black hexagon with the square dot pattern in the middle. The timing is no coincidence, because it means that as soon as the Living Molecules app gets through the appstore review process, the following workflow will be possible:
Of course, using many of the content creation apps the data can be created on a mobile device as well, but adding the feature to SketchEl now makes that a choice: create content on mobile or desktop, whichever is most convenient at the time. And it’s not just for making posters either, but that is one of the original use case proposals.
The molsync.com sharing page has a new feature, as shown on the screenshot to the right (click on it to see the live version): there’s now a black hexagon with a grid pattern in the middle, which is a molecular recognition glyph designed to work with the Living Molecules app. The simplest way to describe it is that it’s a molecular QR code, suitable for inclusion on posters or various other documents. The content can be accessed by using the Living Molecules app to “snap” the glyph, after which it continues on to download the data and make it available for viewing, storing and exporting.
The app has been submitted to the iTunes AppStore, so with any luck, it will be available for download (free) in a week or so!
To view a very early (pre-pre-alpha) demo of the Living Molecules app, check out this YouTube clip. In a nutshell, this app can be used to photograph molecular glyphs, which work like QR codes, except they unlock explicit chemical content. It can view and import the associated chemical data, export it to other apps, and also be used to create molecular glyphs. These glyphs can be included on posters, documents, websites, etc. Continue reading
Cheminformatics 2.0 