And also happy 2024 to everyone, I haven’t been writing much lately on account of juggling work and family life. The topic of this post is two aesthetic molecule drawing improvements that could be described as highly unfavourable from the point of view of the effort:reward ratio, but sometimes these things just bother you for long enough that they bubble up to the top of the to-do list. The first one is split wedges: If you look carefully, the structure on the left has a wedge bond that terminates in an isosceles triangle, and has two single bonds emerging from it, which leaves a little gap ..read more

WebMolKit is a cheminformatics library that I’ve been working on for a long time: it runs on all kinds of JavaScript engines (browsers, desktop via Electron, command line via NodeJS). Its flagship feature is a powerful chemical sketcher, but it also has many supporting functions for handling molecules. As of now, the licensing terms have been switched to Apache 2.0, which basically means you are allowed to use it for non-open projects, as long as proper credit is given ..read more

After much procrastination, there’s an updated demo of the WebMolKit sketcher on the main home page for Molecular Materials Informatics. The sketcher is open source, runs on any web platform, and has some fairly powerful functionality built into it. The sketcher is part of the WebMolKit project, which has been open source for quite some time: it has a lot of molecular manipulation functionality as well as the ability to draw molecules, and is one of the most advanced cheminformatics projects that is 100% web based, being written in TypeScript and cross-compiled to work on any JavaScript-based ..read more

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. I would wager that this increasingly bright spotlight on data quality has a lot to do with the grandiose promises of the current wave of machine learning tools for drug discovery (also known a ..read more

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). A lot of the work I’v ..read more

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. Most people who have dabbled with cheminformatics are familiar with the InChI identifier which is widely considered the best of breed way to “name” a structure by turning it into a canonical string, meaning that any two ways that a chemist may choose to draw a molecule resu ..read more

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. About a year ago we published some of our work on chemical mixtures in Journal of Cheminformatics that we have been doing at Collaborative Drug Discovery. The article describes our efforts to date to define a straightforward common file format for capturing mixtures in a machine readable way, and some o ..read more

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. The third in this cheminformatics from quarantine series involves construction of a second model, which complements the original fragment binders. This was made possible due to the release of public data by Chemical Abstracts regarding structures of anti-viral compounds. The release description states that there a ..read more

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. Yesterday’s description of recent activities in the cheminformatics man-cave described the markup of fragment-like molecules bound to an important COVID-19 protein to build Bayesian structure-activity model. At the end I mentioned that the last section’s enumeration of proposed & scored molecules had a back-story of its own. So here it is. The basic idea ..read more

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. Like almost every other human on the planet (how often do we get to use that phrase non-ironically?), I have been self-isolating and nervously keeping an eye on the statistics, as the global infection rate shows no sign of slowing down anytime soon. Recently we have started to see some of the fruits of hard-won experimental data make its way onto the internet ..read more