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The Latest on Protein Folding
The results of the biannual CASP (Critical Assessment of Structure Prediction) effort have been released. This is a widely-watched competition between different groups (and different programs, methods,...
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Virtual Screening – As Big As It Currently Gets
This new paper on “ultra-large” virtual screening is well worth a look in detail. We find a great many lead compounds in this business by random screening of compound libraries, and virtual screening...
View ArticlePredicting – Or Not Predicting – New Materials
We chemists would love to be able to do just a tiny bit less chemistry now and then and just let models and simulations tell us what would happen instead. Only every once in a while – you wouldn’t want...
View ArticleA Close Look at Fragments
Here’s a look from the D. E. Shaw research team at fragment binding, and even if you don’t do fragment-based drug discovery, it’s worth a read. That’s because the mechanisms by which fragments bind to...
View ArticleComparing Compound Collections
A common question – well, it should be a common question, anyway – is “How do I make sure that this compound collection is a useful one to screen?” There are alternative forms that come down to the...
View ArticleFarewell to “Watson For Drug Discovery”
STAT is reporting that IBM has stopped trying to sell their “Watson for Drug Discovery” machine learning/AI tool, according to sources within the company. I have no reason to doubt that – in fact, I’ve...
View ArticleAn Intro to Deep Learning
I wanted to mention a timely new book, Deep Learning for the Life Sciences, that I’ve received a copy of. It’s by Bharath Ramsundar at Computable, Peter Eastman at Stanford, Pat Walters at Relay, and...
View ArticleAntibody Design, Publicly Challenged
Comes now some rather disturbing news in the antibody field. These things are extremely important, both as therapeutics and as research reagents, and developing them for either purpose is no stroll...
View ArticleThe Cyclofluidic Story
The recent post here on automation in chemistry (especially medicinal chemistry) is a good intro for this paper in ACS Med. Chem. Letters. It’s from David Parry, who led Cyclofluidic, and I’ve blogged...
View ArticleLilly’s Virtual Med-Chem Assistant
Here’s an interesting new paper from Lilly (brought to my attention by Ash Jogalekar on Twitter). “Creating a virtual assistant for medicinal chemistry” is the title, but fear not: this is not...
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Machine-Mining the Literature
We’ve made it to the point – a while back, actually – where people who actually know the subject roll their eyes a bit when the term “artificial intelligence” is used without some acknowledgment that...
View ArticleGet Ready to Recalculate
Here’s a new paper on ChemRxiv that is very much worth reading if you’re a computational chemist (or work with them). And it makes a larger point that’s applicable to everyone else – not an original...
View ArticleText-Mining: Preparing for Battle in India
Since I was just blogging the other day about a machine-learning paper that worked its way through decades of abstracts for materials science papers, this news is timely. Carl Malamud and a team at...
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Saturated Heterocyclic Rings And Their Personalities
Here’s a ring system that you’ve never used before – the cyclopropyl system in purple at the end of the row in the diagram at right. It’s described in this paper from GSK-Stevenage as a new morpholine...
View ArticleRobotic Flow Synthesis: The Latest Version
Here’s another step along the way to automated synthesis, in a new paper from MIT. The eventual hope is to unite the software and the hardware in this area, both of which are developing these days, and...
View ArticleHas AI Discovered a Drug Now? Guess.
Here is an interesting paper in Nature Biotechnology on computational drug design, and if you read it without reading any of the accompanying articles about it, you will have a perfectly good time....
View ArticleAnd Now For A Bit of Quantum Mechanics
OK, today’s blog post is going to be even weirder than usual – we’re going to wander off into quantum mechanics. And into a particular borderland of it where have been a lot of interesting hypotheses...
View ArticleWhat’s Crucial And What Isn’t
One of the reasons that people in or near this business can write such gaudy press releases is that it has so many moving parts. That lets everyone claim that the part that they’re addressing is...
View ArticleAn AI-Generated Drug?
There were some headlines the other day about the “first AI-discovered drug”, so that should send us to the work in question to see what’s going on. The company in question is called Deep Genomics, and...
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Down Amongst the Water Molecules
This new paper shows one reason why it’s so tricky to calculate compound binding in an active site (which is what we’d want to do in order to do effective in silico virtual screening). The authors (a...
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