The Limits of Big Data
I fear that mentioning the phrase “Big Data” in the first sentence of a blog post will make half the potential readers suddenly remember that they have podiatrist appointments or something. But that’s...
View ArticleClik here to view.
Calculating A Few Too Many New Compounds
The phrase “automatic chemical design” will generally get my attention, especially when it’s applied to drug-like molecules. And that’s one the the key parts of this paper, from researchers at Harvard,...
View ArticleClik here to view.
David Weininger and Chemical Names
David Weininger passed on last week, and you probably have to be into chemoinformatics for that name to immediately register. He came up with the SMILES notation for chemical structures, though, so...
View ArticleNitration Isn’t So Simple
OK, let’s get physical organic here for a little while. For those outside the field, physical organic chemistry is the branch that studies how and why the reactions of organic chemistry happen – the...
View ArticleWatson and Pfizer
I have wondered several times around here about how (and if) IBM’s Watson platform is going to be able to help out with drug discovery, and it looks like we may be able to find that out. Pfizer has...
View ArticleUnicorn Software for Drug Discovery
So here’s the dream. You sit down at the keyboard and load a file of the structure of your new drug target – you’ve discovered that inhibition of Whateverase II or a ligand for the Type IV Whazzat...
View ArticleClik here to view.
The Flightosome
I got this diagram from Arjun Raj‘s Twitter feed, and I think I enjoy it a bit more every time I see it. Some of that is because it’s a big part of what I was trying to get across in this column, but I...
View ArticleAn IBM-Watson Collaboration Goes Under
I’ve written several times about IBM’s Watson machine learning system and its potential applications to health care. To be honest, many of these applications sound unlikely, at least at present, and...
View ArticleClik here to view.
The Microbiome and Human Obesity: Wait a Minute
For the last few years, it has been impossible to escape talk of the microbiome – the associated bacteria (and other organisms) that live in and on the human body. Overall, this attention has been a...
View ArticleThe ACS Journals Tighten Up Screening Standards
Here’s an article (free access) in ACS Central Science on assay interference compounds, a contentious topic that has been aired here (and in many other places). This one, though, is authored by the...
View ArticleFree Compounds, Chosen By Software
Here’s how the press release starts, and I’ll say this for it, it does get the reader’s attention: “Atomwise Inc. seeks proposals from innovative university scientists to receive 72 potential...
View ArticleSoftware Eats the World, But Biology Eats It
I can strongly recommend this Bruce Booth post at LifeSciVC on computational models in drug discovery. He’s referencing Marc Andreessen’s famous “Why Software Is Eating the World” essay when he titles...
View ArticleClik here to view.
Model This?
Via Ash Jogalekar on Twitter, I came across this new paper from researchers at AstraZeneca (and collaborators in Sweden, the UK, and Denmark) on the synthesis and activity of some plasmin inhibitors....
View ArticleNature Doesn’t Abhor a Vacuum As Much As You’d Think
I wrote some years ago about the case of a protein that seemed to have a completely empty binding pocket – empty, as in not even any water molecules hanging around in there. There are a number of these...
View ArticleKnock Six Years Off Your Timeline. Um.
There’s only one honest answer to the question “How long does it take to develop a new drug?”, and that’s “Too @#$! long”. In the same way, the only honest answer to “What are the average chances for a...
View ArticleClik here to view.
Stereochemical Mysteries, Solved
Ask a chemist (I’ll do) about optical rotation, and you’ll get a confident answer about how right- and left-handed isomers of chiral compounds will rotate polarized light that shines through a solution...
View ArticleReading the Minds of Medicinal Chemists
I suppose that all of us medicinal chemists should be flattered by this press release. According to it: Medicinal chemistry is among one of the most important and intellectually-challenging professions...
View ArticleObjections to (Some) Drug Discovery AI
Here’s a piece to start some arguing: “AI in Drug Discovery is Overhyped”, by Mostapha Benhenda. I realize that a lot of people will read that title and go “Well, yeah, sure”, but it’s definitely worth...
View ArticleClik here to view.
Way Down There in the Pores
Let’s get physical-organic. A big topic of research in recent years has been the properties of liquids and solids under boundary conditions. By that sweeping statement, I mean questions such as “When...
View ArticleClik here to view.
Retrosynthesis: Here It Comes
Behold the rise of the machines. It’s been going on for a while, but there are landmarks along the way, and we may have just passed another one with the publication of this paper. It’s open-access,...
View Article