Images of Machine Learning
Where has machine learning made the most strides in recent years? A lot of people who are into this topic will tell you that it’s image processing, specifically recognition and differentiation of...
View ArticleDown At the Crystal Surface
If you’re at all involved in producing solid forms of compounds, you’re familiar with the concept of a polymorph. That, put simply, is a different crystalline form, and any given substance can have...
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The Rise of the Rise of the Machines
There’s yet another paper on computer-devised retrosynthesis out today – it and the previous one make an interesting pair. I have a Nature “New and Views” comment on this one (free access link) for a...
View ArticleBenevolentAI: Worth Two Billion?
Regular readers will know that I have no problem believing that AI (in its various forms) will definitely have an impact on drug discovery. And regular readers will also know that I’m quite skeptical...
View ArticleCalculate Your Way Out of Bad Yields
I wrote a little while back about a brute-force approach to finding metal-catalyzed coupling conditions. These reactions have a lot of variables in them and can be notoriously finicky about what...
View ArticleRelay Calculates Its Way Through
Bloomberg has a feature on Relay Therapeutics, who are just a few blocks away from me (and where several former colleagues of mine work). It’s a nice writeup, and also features a (relatively rare)...
View ArticleAI Will Not Threaten Pharma Patents – Not This Way
I’d class this letter to Nature as “interesting but wrong”. Here’s the argument: . . .A patent is granted only when a compound’s application can be classified as both ‘new’ and ‘invented’. A highly...
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The Entropic Term is Laughing At Us
There are plenty of things to optimize in a med-chem project other than binding affinity. But if you don’t have at least some level of binding, you may not have a med-chem project. And while from the...
View ArticleA Retrosynthesis Contest
Here’s a retrosynthesis challenge from Merck KGaA in Darmstadt. They’re celebrating the company’s 350th anniversary, and this is apparently part of the festivities. Anyone can enter for free, and the...
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The Case of Verge Genomics
A number of people have passed along the recent press stories about Verge Genomics, a new company out of YCombinator that has just raised $32 million for neuroscience drug discovery. Now that, as...
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Automated Reaction Discovery Gets Smarter
Here’s an interesting paper from the Cronin lab at Glasgow. It’s titled “Controlling an organic synthesis robot with machine learning to search for new reactivity”, and that title alone will make some...
View ArticleMachine Learning’s Awkward Era
The whole machine learning field has a huge amount to offer chemistry, medicinal chemistry, and biomedical science in general. I don’t think that anyone seriously disputes that part – the arguing...
View ArticleVirtual Compound Screening: The State of the Art
Here’s an interesting article from a former colleague of mine, Pat Walters, on virtual chemical libraries. Those, of course, are meant to fill in the (large, enormous, humungous) gap between “compounds...
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Simple Rings, Simply Wrong
Medicinal chemists spend a lot of time thinking about the relative greasiness of their molecules. Being professional scientists, of course, we have come up with some slightly more quantitative phrases...
View ArticleRewiring Plankton. And Reality.
OK, the “Silicon Valley Meets Biotech” subject has come up around here numerous times, most recently here, about a startup out of YCombinator called Verge Genomics. But several people have called my...
View ArticleDrug Repurposing, Computed
Here’s an example of something that we’re all going to see more of in the coming years: the computational approach to biochemical pathway discovery and (potentially) new therapies. In this case, the...
View ArticleLigand Efficiency Rethought
Peter Kenny has a paper out on ligand efficiency that’s required reading for medicinal chemists using (or thinking about) that concept as a design tool. I’d recommend reading it with this recent paper...
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A Magic Methyl, Spotted in the Wild
You hear medicinal chemists talking about the “magic methyl”, the big effect that a single CH3 group can have on potency or selectivity. Here’s a new J. Med. Chem. paper that shows one in action.That...
View ArticleHere’s What’s Been Done Before
I enjoyed this ACS Med. Chem. Letters perspective on AI and machine learning in medicinal chemistry. It has several good points to make, and it brought up one that I haven’t gone into here before: if...
View ArticleMachine Learning: Be Careful What You Ask For
Let the machine learning wars commence! That’s my impression on reading over the situation I’m detailing today, at any rate. This one starts with this paper in Science, a joint effort by the Doyle...
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