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Posts tagged with "In Silico"

  • In Silico

    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, 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

    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

    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

    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

    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

    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.

    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

    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

    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

    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
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