What’s in a name: Molecular Materials

I am presently attending the Gordon Research Conference: Computer Aided Drug Design meeting, having a wonderful time, and at this moment taking an afternoon break to relax and catch up on some work. This is one of my favourite properties of the GRC meeting format, because it means that it’s not necessary to be pretty much out of the loop for the entire week.

So far I’ve met and reacquainted myself with more scientists of my own particular species than I can count, and a recurring theme of the introduction/renewal process is taking turns to explain what we’re both doing these days. One part of this which seems a little incongruous is that the name of the company that I created is called “Molecular Materials Informatics”. Since the occasion is a conference that is exclusively devoted to the pursuit of drug molecules and a few related parts of life sciences, this requires some explanation. Read the rest of this entry »

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Inline abbreviations with XMDS

abbrev1Abbreviations are a common shorthand used by chemists to alleviate the tedium of drawing out structures by hand, and in many areas – including much of organometallic and inorganic chemistry – use of abbreviations is more or less essential to achieve any kind of visual clarity. This presents a challenge for cheminformatics, though, because there is no universal dictionary for abbreviations: different research groups use different shorthand notations for their own nefarious purposes. Now the beta version of XMDS is catching up to MMDS by adding the ability to conveniently define inline abbreviations, which are readable to humans in diagram form, but also completely well defined behind the scenes for the benefit of machines. Read the rest of this entry »

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Closing the collaborative loop: Bayesian models with XMDS, CDD Vault and MMDS

vaultexport13The CDD Vault web product has recently delivered on one of its promises: making models truly sharable to the community, including both open source and participating commercial products. Bayesian models can now be exported in a well documented and openly consumable format, which removes a major bottleneck in the creation and use of models for structure-activity predictions. Read the rest of this entry »

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Always-on R/S and E/Z stereo labels with XMDS

xmds_stereo1The most recent addition to the OS X Molecular DataSheet (XMDS) desktop app is calculation of stereochemistry labels as-you-edit, using the Cahn-Ingold-Prelog (CIP) designations (R/S, Z/E). The labelling can be switched off with a menu option, but since most people use software with its factory settings, this is more or less equivalent to having it hardcoded permanently. Read the rest of this entry »

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Aspects and XMDS: higher order metadata for datasheets

xmds_aspect1Recent progress on the OS X Molecular DataSheet (XMDS) app, which is currently in beta, has involved the inclusion of aspects into the user interface for editing datasheets. The core format that the XMDS desktop app, as well as all the rest of the products from Molecular Materials Informatics, is the datasheet, which is a tabular format made up of rows and columns: like a spreadsheet, except that the columns are strongly typed, so you can’t just abuse it and put in whatever you want wherever you want. The minimalistic table datastructure can be supplemented by any number of aspects, which are directives that impose higher order layers of interpretation, which are often composed of multiple columns (e.g. a chemical reaction which cobbles together multiple molecules for its reactants, reagents and products). One of the fun software engineering challenges has been to make these complex representations fit seemlessly into the grid-based “spreadsheet” editor upon which XMDS operates. Read the rest of this entry »

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XMDS ready for beta phase

xmds_hubThe OS X Molecular DataSheet (XMDS) desktop app is now ready for beta testing. And by beta testing, I mean the minimum viable product is done and ready to be used for actual cheminformatics tasks. You can sign up anytime: all it takes is an email (info@molmatinf.com), a Mac with Yosemite-or-later (v10.10), and a Dropbox account. And you get to keep using the app for as long as you want, even after the beta testing programme is wrapped up. Read the rest of this entry »

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Literature how-to for structure:activity Bayesian models (and open source)

bayesianA two-pack of publications in Journal of Chemical Information and Modeling is now available: Bayesian the first, and Bayesian the second. Both papers are open access, so by all means go read them instead of this blog post. The first paper details the implementation of a variation of the classic naive Bayesian method that is suitable for use with structure-derived fingerprints such as ECFP6 and FCFP6. The text goes into some detail about how it is implemented, to the point of including pseudocode, which complements the fact that the source code is available as part of the Chemical Development Kit (CDK), conveniently and concisely coded up in a single source file. The intention is quite unashamedly to tell you everything you need to know to build the algorithm from scratch, should you be so inclined; and if not, to understand every little detail about how the open source software works. The second paper goes into some more detail about how to use this kind of (“Laplacian-modified”) Bayesian model, including a calibration method, and an extensive study carried out by extracting thousands of model-ready datasets from the ChEMBL database. Read the rest of this entry »

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