cheminformatics

BioAssay Express: finding assays (and doing stuff with them)

bae_find04The BioAssay Express project has been moving forward at a solid pace: several important new features have been added or improved for locating assays and inspecting them, with an eye toward performing some sophisticated analysis and model building. This is motivated by the fact that we have curated quite a few assays (~3,500) which is sufficient reason to start putting real effort into figuring out what we can actually do with this high quality professionally annotated data. Continue reading →

Green Solvents app: complete facelift

greensolv_dev1Way 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. Continue reading →

Reaction similarity searching with MolSync

reaction_similarity1To 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. Continue reading →

MolSync overhaul: back to the web, now with reactions too

molsync_overhaul1Things have been a bit quiet in these parts lately, but not due to inactivity: far from it. In between working on some exciting projects with Collaborative Drug Discovery, I have been quietly making rapid progress on several important key technologies. These include the OS X Molecular DataSheet (XMDS), presiding over a growing collection of reaction data, and most recently a complete overhaul of the MolSync website, which provides cheminformatics support services of various kinds. Continue reading →

XMDS experiments: quantities, metrics and SVG

editexperiment8The XMDS molecular datasheet editor is steadily marching forward in terms of functionality: the reaction scheme editor has been complemented by separate display panels showing the quantities of each component in blocks, which can be opened up and edited. The green chemistry metrics (PMI, E-factor, atom economy) are also calculated and shown. In the interests of making the data useful for presentations, bitmapped or vector representations can be dragged directly into a graphics package (e.g. Pages, Word, PowerPoint, Keynote, etc.), and generation of SVG images is now supported, so reactions and molecules can be easily touched-up with a vector graphics editor like Inkscape. The XMDS app (for Mac OS X) is still in long beta, so you are welcome to try it out (just ask nicely). Continue reading →