Is FEP Ready For the World?
Here’s a paper that basically throws down the computational gauntlet. A large group of authors from Schrödinger, Nimbus, Columbia, Yale, and UC-Irvine say that their implementation of free energy...
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Neural Networks for Drug Discovery: A Work in Progress
There have been many attempts over the years to bring together large amounts of biological and drug activity data, winnow them computationally, and come up with insights that would not be obvious to...
View ArticleDiversity and Similarity Scoring: Does One Size Ever Fit All?
We spend a lot of time talking about compound similarities in this business. All those schemes for virtual screening, to find new activities for old compounds, to predict side effects and general...
View ArticleNot Even Wrong
This paper is not going to make a lot of computational chemists very happy at all. It’s from Dan Singleton and Erik Plata at Texas A&M, and it’s on the Morita-Bayliss-Hillman reaction. More...
View ArticleA Couple of Ycombinator’s Startups
Last year I mentioned reports that the startup incubator Ycombinator was thinking of getting into the biopharma field. Here’s a look at the current crop of potential companies. One thing that stands...
View ArticleSanofi Bets on Schrödinger
Sanofi has signed an expanded deal with Schrödinger, the computational chemistry folks. Here’s something from the press release: Schrödinger has made a number of key scientific breakthroughs in recent...
View ArticleLevels of Data
Here’s a brief article in Science that a lot of us should keep a copy of. Plenty of journalists and investors should do the same. It’s a summary of what sort of questions get asked of data sets, and...
View ArticleUsing the Same FEP Ruler
With free energy perturbation having its time in the calculational spotlight, thanks to Schrödinger and others, it seems worthwhile to link to this new paper. It’s a proposal for a common framework to...
View ArticleArtificial Intelligence For Biology?
A new paper in PLoS Computational Biology is getting a lot of attention (which event, while not trying to be snarky about it, is not something that happens every day). Here’s the press release, which I...
View ArticleModeling the Rats, Who Model the Humans
When you get down to it, one of the biggest problems in drug discovery is that there is (in most cases) no alternative but doing things the hard way. If you want to find out if your drug is going to...
View ArticleArtificial Intelligence, You Say?
Here’s a story from the Telegraph about a small company (Berg Pharmaceuticals), whose headline certainly got my attention: “Cancer drug development time halved thanks to artificial intelligence”. That...
View ArticleNot Quite There Yet
I’ve been meaning to blog about this paper, because its abstract certainly promises a lot: . . .Target prediction software based on machine learning models correctly identified additional...
View ArticlePattern-Matching Binding Sites
Here’s a recent paper that bears on the “How many binding pockets are there” question. Or maybe that’s the “How many different types of binding pockets” question, which last came up around here a...
View ArticleOne Step Beyond! Maybe More.
There are plenty of useful drugs whose structures are, well, odd-looking. Antibiotics, as a class, have a lot of these: macrocycles, polyenes, polyhydroxylated beasts that don’t fit in with a medicinal...
View ArticleClouding Biology: That Verb Cuts Both Ways
Here’s Steve Dickman at Forbes with a look at “cloud biology” approaches to medicine and drug discovery. This is an area I’ve written about several times before, and I also recommend Wavefunction’s...
View ArticleA Terrific Paper on the Problems in Drug Discovery
Here’s a really interesting paper from consultants Jack Scannell and Jim Bosley in PLoS ONE, on the productivity crisis in drug discovery. Several things distinguish it: for one, it’s not just another...
View ArticleMore Binding Sites Than Are Dreamt of in Your Philosophy
Cryptic binding sites: now there’s a puzzle for you. When you look at a protein structure, even if you know nothing about its function, you can usually spot small-molecule binding sites without too...
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The Algorithms Are Coming
I think that every synthetic organic chemist should take a look at this paper in Angewandte Chemie. It’s on the application of computer algorithms to planning synthetic routes, which is a subject...
View ArticlePredicting New Reactions
While working on my talk on robotics and artificial intelligence, I was sent a link to this paper (PDF) which I thought was worth a look. It’s from a team at the University of Münster, and what they’re...
View ArticleBetter, Faster, More Comprehensive Manure Distribution
So today brings news that Microsoft is working on curing cancer in the next five or ten years. That, I’m sure, will come as a relief, especially to those people who’ve had the company’s software crash...
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