The Journal of Cheminformatics is organising a Special Collection entitled “Biomedical Data Analyses Facilitated by Open Cheminformatics Workflows” which encourages researchers to publish their workflows for gathering, preparing, curating and cleaning data. This resonates well with a growing explicit awareness within the community that data quality isn’t just an important thing, it’s the important thing.

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In the spring of 2021, writing from the comfort of my home office, it’s hard to even remember what it’s like to pack my bags and head out to stand in front of a room and tell people about what I’ve been doing lately. The delights of airport security, jetlag, hotel wifi and bad coffee are not exactly missed, but pretty much everything else is. Results do still get communicated, though, and one nice thing about delivering a webinar is that you can be pretty sure it will be recorded for the benefit of the whole internet for all time (or as may be the case, some of the time).

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About a year ago I described the results of a preliminary project to scope out the possibility of making the InChI identifier play nice with inorganic & organometallic complexes. There’s now a followup increment that does likewise for some of the higher valence stereochemistry centres that are found in these complexes.

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Drawing chemical mixtures can be done online, with a conversion feature to generate Mixtures InChI (MInChI) notation. Pseudomixtures from Molfiles are now enumerated automatically when pasted in. The tools for working with machine readable mixtures, using the web platform, are open source. Continue reading →

A newly available collection of antiviral structures from Chemical Abstracts has been made available, and has now been shoehorned into a model that can be used online to evaluate potential antiviral drug candidates for COVID-19. The tool can be found at https://molmatinf.com/covid19. Continue reading →

Further to yesterday’s post about making model resources for COVID-19 available online, the resource page now shows the reaction transforms used to propose potential new candidates, as well as atom highlighting for applied Bayesian models. Continue reading →

Structure-activity datasets for small molecules targeting the global COVID-19 pandemic are starting to emerge. Some preliminary modelling and interactive tools based on one of these datasets is available at https://molmatinf.com/covid19. Continue reading →

The BioAssay Express project captures a lot of public bioassay data using public ontologies, and quite often these ontologies overlap with each other: this happens particularly often with the target concept. We needed to map common terms between the Drug Target Ontology and Uniprot (via the Protein Ontology) with a mapping file. The amount of data involved was a little too much to do manually, but not quite enough to justify writing a custom script. Because it had to be done exactly once, the task was an ideal use case for Excel. Continue reading →

As part of spring cleaning for the new decade of 2020, the website for Molecular Materials Informatics has been re-done. The original plan for the site in 2010 was to make it information rich, but a lot of it had gotten stale over the years: products appear, disappear and change. Now it’s more of a placeholder with links to projects that have their own sites wherever possible, e.g. documentation and open source projects are hosted on GitHub.

Lately I’ve been working on a new extension to the InChI identifier which is intended to broaden its domain to include the universe of non-organic compounds and all of the insane diversity of exotic bonding types. Preliminary results of the first stage are up on GitHub. Continue reading →