NIH probe molecules in the Approved Drugs app

appvdrugs_probesSince the relevant paper just became available (“The parallel worlds of public and commercial bioactive chemistry data”, Lipinski et al, Journal of Medicinal Chemistry), now is as good a time as any to mention that the NIH probe molecules discussed in the article have been incorporated into the latest version of the Approved Drugs app.

The so-called “probes” are molecules screened by the NIH Molecular Libraries Program, having been deemed to be excellent starting points for designing drugs, according to all contemporary medicinal chemistry lore. As is so often the case in this industry, searching for a simple datafile on the open internet that contains the constituent datafile, with all the structures carefully curated and checked and matched to the corresponding identifiers, comes up inconclusive. This collection has now been assembled in an easily digestible form, and so it is no longer necessary to crawl through long PDF files and reenter everything:

The Probes now make up a second group of structures, as shown on the screenshot to the top right. These can be perused, filtered, searched, exported and clustered in the same way as the regular list of drug molecules.

On another note, the similarity method used for sorting molecules by comparison to a reference compound, and for dynamic clustering, has been switched to the ECFP_6 fingerprint implementation that was created for the Chemical Development Kit, and subsequently the TB Mobile app.

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Mobile sketcher overhaul in progress

sketchmmds_ipadThe molecular drawing capabilities introduced with the Mobile Molecular DataSheet (MMDS) app are still unique in the mobile chemistry space insofar as the user interface allows for precise drawing of manuscript-quality diagrams (i.e. perfect bond lengths and angles), on an incredibly tiny screen (the original iPhone form factor), and also very quickly. This sounds like a violation of basic engineering principles (i.e. fast, cheap, good: pick two), but there is of course a down side: the interface is different from the conventional industry standard paradigm, and takes some getting used to. While the capabilities have been regularly improved over more than 4 years since it was first released, a significant overhaul of the “onboarding” experience is long overdue, starting with more targeted adaptation to multiple screen sizes. Read the rest of this entry »

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Second impressions of Swift: making Objective-C look good

I held off writing this post since Apple’s new Swift language was at version 1.0, and it was clearly rushed to market/probably should’ve stayed in beta for quite awhile longer, but now that 1.1 is out, I can say that things are not looking good from a performance point of view. The reason I was excited about the language from the moment I read the specification (other than wanting to see the end of Objective-C) is that the design takes into account the notion of having a clean high level syntax that provides enough information for the compiler to understand what is, and isn’t, trying to be accomplished in a given block of code, and optimise accordingly. A reading of the spec suggests that Swift is, among other things, a better Java: all the safety and convenience of bounds checking and automatic memory management, but with clever ways to reduce or eliminate the performance penalties that come with it. Read the rest of this entry »


The Beer Lab Notebook

bln_snap1Today another of my apps just got through onto the store: the Beer Lab Notebook, which can be found on the iTunes AppStore. The name of this app is inspired by the title of my last new app (the Green Lab Notebook): its subject material is more or less serious, depending on your priorities. The app is designed to help record the process of creating a fermented beverage, as practiced by millions of homebrewers, myself included. Read the rest of this entry »

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Impressions of Apple’s Swift, after a bit of practice

Lately I’ve been getting my feet wet learning the latest new programming language from Apple that everyone is talking about: Swift. The short conclusion is that it’s pretty good, but unsurprisingly has quite a collection of glitches: some of them are fixable, some of them are annoying arbitrary choices that I’ll get used to, and others are probably more like design flaws that are unlikely to ever go away. I’m cautiously optimistic that the latter category is fairly short, though still too early to call it. And because Swift is such a new language – hot out of the oven, as it were – I was not inclined to rush in and start coding up anything that’s directly important to my company’s cheminformatics software stack, so instead decided to take a little detour and make a new app from scratch: something fun, that I’ve been meaning to do for ages, called the Beer Lab Notebook, written entirely in Swift, with no non-Apple dependencies. But more about that particular project in a later post. Read the rest of this entry »

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ChemSpider Mobile 2.0 is out!

AppIcon1024After a good long while in development, version 2 of the ChemSpider Mobile app is now available on the iTunes AppStore. As one would expect from an increment of the major version number, the new release is a major overhaul, starting with an entirely new aesthetic which splits the difference between the iOS 7 mojo and the contemporary branding of the Royal Society of Chemistry, which owns and operates the ChemSpider service. Read the rest of this entry »

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Sharing experiments: using ChemSpider Synthetic Pages examples and a trip down memory lane

exptshare0Now that the service has been upgraded so that it can produce human-readable pages with experiment details generated by the Green Lab Notebook app, it is time to demonstrate some of these. The snapshot to the right shows a screen grab of a collection of experiments that were manually keyed in from the ChemSpider Synthetic Pages service. Unlike the original data, though, the schemes have been carefully constructed so that each and every atom is accounted for in the chemical structure representations, and whenever possible all byproducts are accounted for, all stoichiometric reagents are correctly balanced, and quantities are entered in a standardised form. Read the rest of this entry »

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