3 ms·
It's important to note that although chemical space is quite large, most of this space is not easy to synthesize and also is not chemically feasible, stable or
by gpcr1949 5y ago
It's important to note that although chemical space is quite large, most of this space is not easy to synthesize and also is not chemically feasible, stable or desirable. Another interesting "small" subset of chemical space is ZINC [0] which is a database of about a billion commercially offered compounds, meaning that manufacturers at a minimum think they can easily make them (and effectively the fulfilment is quite high when random compounds are ordered, e.g. 95% in this paper where they did molecular docking simulations on the entirity of this database to find new melatonin receptor modulators [1]). Concerning exploration of chemical space, one area that might be of interest here is the quite effective smooth(ish) movement through structure-property space using VAEs.[2]
[0] https://zinc.docking.org/ https://zinc.docking.org/
[1] "Virtual discovery of melatonin receptor ligands to modulate circadian rhythms" https://www.nature.com/articles/s41586-020-2027-0.pdf https://www.nature.com/articles/s41586-020-2027-0.pdf
[2] "Automatic Chemical Design Using a Data-DrivenContinuous Representation of Molecules", https://arxiv.org/pdf/1610.02415.pdf https://arxiv.org/pdf/1610.02415.pdf
- jhirshman 5y agoWe've been working on these types of chemical search optimizations problems across a variety of industries, and I'd like to echo this comment. Despite the fact that most of the space is unexplored, the act of exploring it for the sake of exploring it is often unwise. A vast, vast majority of the time a naive or even statistically driven search will fail if the goal is to find something "new." The reality is that the path to a truly new innovative chemical is hard to anticipate and even harder to optimize for plus the curse of dimensionality means that our intuition for how hard that search really is is hopelessly misguided. If you're interested in related problems, my company, Uncountable, is looking for software engineers. https://www.uncountable.com/careers https://www.uncountable.com/careers. We emphasize that the most important thing for organizations to do today is structure their data. It's the best chance to take specialized internal knowledge and put it to use to find new chemicals.