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. Continue reading

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. Continue reading

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. Continue reading