Automated Discovery
To what extent can scientific discovery be automated? Where are the areas where automation can make the biggest contribution to human efforts? These questions and a number of others are addressed in a...
View ArticleSimulation and Understanding
Roald Hoffmann and Jean-Paul Malrieu have a three-part essay out in Angewandte Chemie on artificial intelligence and machine learning in chemistry research, and I have to say, I’m enjoying it more than...
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How To Deal With Machine Learning Papers
Here’s a very useful article in JAMA on how to read an article that uses machine learning to propose a diagnostic model. It’s especially good for that topic, but it’s also worth going over for the rest...
View ArticleOnly Connect
Anyone who’s done fragment-based drug design (especially) or who has just looked at a lot of X-ray crystal structures of bound ligands will be able to back up this statement: if you sit down with a...
View ArticleWill It Learn? Can It Learn?
OK, we’re going to get a bit esoteric this morning. There are all kinds of things going on in the world, but I’m going to seek refuge for a little bit in abstraction, and if that’s your sort of thing,...
View ArticleAnother AI-Generated Drug?
I see that there’s press coverage today of “the first AI-generated drug” to go into human trials. Some will recall this similar claims have been made before, so what exactly are we looking at? The...
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Arguing on AI Drug Discovery
Here’s a letter from Pat Walters and Mark Murcko of Relay Therapeutics on the September report from Insilico Medicine (blogged here) of a drug discovered by AI, specifically generative methods. Here’s...
View ArticleMachine Learning for Antibiotics
I know that I just spoke about new antibiotic discovery here the other day, but there’s a new paper worth highlighting that just came out today. A team from MIT, the Broad Institute, Harvard, and...
View ArticleTwo Tribes
I’m sitting in an MIT conference on AI in drug discovery/development as I write this. One of the speakers here (Mathai Mammen, J&J/Janssen) just made a good point – not a new one, but a solid one...
View ArticleCalculating Your Way to Antivirals
My intent is to start mixing in some non-coronavirus posts along with my pandemic science coverage – you know, like the blog used to be way back earlier in the year (!) Today’s subject might be a good...
View ArticleMachine Learning On Top of DNA Encoded Libraries
DNA-encoded libraries are a technique that many in the field should be familiar with, and they’ve come up many times here on the blog. The basic idea is simple: you build up a set of small molecules...
View ArticleAI, Machine Learning and the Pandemic
It’s not surprising that there have been many intersections of artificial intelligence and machine learning with the current coronavirus epidemic. AI and ML are very hot topics indeed, not least...
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Generating Crazy Structures
I feel like a dose of good ol’ organic chemistry this morning, and a (virtual) meeting I attended yesterday gave me a paper to talk about that delivers some. I was speaking with a local group of...
View ArticleProtein Folding, 2020
Every two years there’s a big challenge competition in predicting protein folding. That is. . .well, a hard problem. Protein chains have (in theory) an incomprehensibly large number of possible folded...
View ArticleAI and Drug Discovery: Attacking the Right Problems
I’ve been meaning to write some more about artificial intelligence, machine learning, and drug discovery, and this paper (open access) by Andreas Bender is an excellent starting point. I’m going to be...
View ArticleMachine Learning Deserves Better Than This
This is an excellent overview at Stat on the current problems with machine learning in healthcare. It’s a very hot topic indeed, and has been for some time. There has especially been a flood of...
View ArticleMore Protein Folding Progress – What’s It Mean?
I last wrote about Deepmind’s efforts to predict protein folding and structure here, with their AlphaFold software. AlphaFold really performed very strongly in the 2020 protein folding challenge, and...
View ArticleA New Antibody-Dependent Enhancement Hypothesis
Here’s another post that I will regret writing, but a great many people have asked me about a new preprint that brings up the possibility of antibody-dependent enhancement with the current vaccines and...
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