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. Read the rest of this entry »

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MolSync reaction searching: atom mapping

molsync_atommap0The latest unit of progress for the 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 »

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MolSync reaction searching: basic pieces in place

molsync_rxnsrch1The last update of the MolSync site added a visual overhaul and molecule searching. Today’s update brings along the basic UI for reaction searching, and preliminary functionality for various kinds of reaction searching by structure. Read the rest of this entry »

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MolSync site with visual overhaul

molsync_newlook1As mentioned in previous posts, the MolSync site has had a major redesign under the hood, and now it has been followed up with an aesthetic re-skinning. The presentable web content was always presented as somewhat of a placeholder, since the main purpose of the site was to expose certain cheminformatics and data hosting capabilities, in particular to boost the functionality of various mobile apps. Now that it is evolving into a site that provides user-facing functionality as well, it is time for a little bit more attention to detail on the design front. Read the rest of this entry »

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MolSync web structure searching

molsync_search1As mentioned in the previous post, the MolSync (.com) website and the technology behind it have been moving forward rapidly. The public-facing deployment now shows a proof of concept page for performing molecule searches: Read the rest of this entry »

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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. Read the rest of this entry »

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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). Read the rest of this entry »

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