Derek Lowe's commentary on drug discovery and the pharma industry. An editorially independent blog from the publishers of Science Translational Medicine. All content is Derek’s own, and he does not in any way speak for his employer.

By Derek Lowe

Posts tagged with "In Silico"

• In Silico

  The Latest on Protein Folding

  3 December, 2018

  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, hardware, etc.) to see how well protein structures can be predicted de novo from just the protein sequences themselves. In the main category, the or… Read More

• Chemical News

  Machine Learning: Be Careful What You Ask For

  20 November, 2018

  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 group at Princeton and Merck, which used ML techniques to try to predict the success of Buchwald-Hartwig coupling reactions. The idea… Read More

• Chemical News

  Here’s What’s Been Done Before

  8 November, 2018

  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 you’re mining the literature, you will get what the literature can tell you. At the very best, the high… Read More

• Drug Assays

  A Magic Methyl, Spotted in the Wild

  7 November, 2018

  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 structure looks like a kinase inhibitor if anything ever did, and so it is. But small changes to it can… Read More

• Drug Assays

  Ligand Efficiency Rethought

  1 November, 2018

  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 – between the two of them, you’re going to have references to a huge swath of the literature on how to measure… Read More

• Cancer

  Drug Repurposing, Computed

  26 October, 2018

  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 authors are looking at some pretty intractable tumor types (type 3 and type 4 medulloblastoma), which is a good place for discovery in… Read More

• Chemical Biology

  Rewiring Plankton. And Reality.

  24 October, 2018

  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 attention to this proposal over at (yes) YCombinator, so by gosh, it’s coming up again. Because this is just too much to believe. Read More

• Chemical News

  Simple Rings, Simply Wrong

  26 September, 2018

  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 than “relative greasiness”, but that’s definitely the idea. How hydrophilic/hydrophobic a compound is determines not to what extent… Read More

• Drug Assays

  Virtual Compound Screening: The State of the Art

  6 September, 2018

  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 that we have on hand to screen” and “compounds that we could screen if we actually had them”. That second group, if ta… Read More

• In Silico

  Machine Learning’s Awkward Era

  8 August, 2018

  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 starts when you ask when this promise might be realized. In the abstract, the idea of tireless, relentless analysis of the huge piles of… Read More