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Posts tagged with "In Silico"

  • Clinical Trials

    Benford’s Law, Revisited

    I mentioned Benford’s Law in passing in this post (while speculating on how long people report their reactions to have run when publishing their results). That’s the rather odd result that many data sets don’t show a random distribution of leading digits – rather, 1 is the first digit around 30% of the time, 2… Read More
  • Drug Assays

    Selective Scaffolds

    We spend a lot of time in this business talking about molecular scaffolds – separate chemical cores that we elaborate into more advanced compounds. And there’s no doubt that such things exist, but is part of the reason they exist just an outcome of the way chemical research is done? Some analysis in the past… Read More
  • Drug Assays

    Why Don’t We Have More Protein-Protein Drug Molecules?

    Almost all of the drugs on the market target one or more small-molecule binding sites on proteins. But there’s a lot more to the world than small-molecule binding sites. Proteins spend a vast amount of time interacting with other proteins, in vital ways that we’d like to be able to affect. But those binding events… Read More
  • Drug Assays

    Side Effects, Predicted?

    There’s a new paper out in Nature that presents an intriguing way to look for off-target effects of drug candidates. The authors (a large multi-center team) looked at a large number of known drugs (or well-characterized clinical candidates) and their activity profiles. They then characterized the protein targets by the similarities of the mol… Read More
  • Current Events

    Warren DeLano

    I’ve been remiss in not mentioning this, but I just found out recently that Warren DeLano (the man behind the excellent open-source PyMOL program) passed away suddenly earlier this month. He was 37 – another unfortunate loss of a scientist who had done a lot of fine work and was clearly on the way to… Read More
  • Chemical News

    The Further In You Go, The Bigger It Gets

    I had a printout of the structure of maitotoxin on my desk the other day, mostly as a joke to alarm anyone who came into my office. “Yep, here’s the best hit from the latest screen. . .I hear that you’re on the list to run the chemistry end. . .what’s that you say?” This… Read More
  • Drug Assays

    Why Does Screening Work At All? (Free Business Proposal Included!)

    I’ve been meaning to get around to a very interesting paper from the Shoichet group that came out a month or so ago in Nature Chemical Biology. Today’s the day! It examines the content of screening libraries and compares them to what natural products generally look like, and they turn up some surprising things along… Read More
  • Biological News

    What’s So Special About Ribose?

    While we’re on the topic of hydrogen bonds and computations, there’s a paper coming out in JACS that attempts to answer an old question. Why, exactly, does every living thing on earth use so much ribose? It’s the absolute, unchanging carbohydrate backbone to all the RNA on Earth, and like the other things in this… Read More
  • In Silico

    Another Thing We Don’t Know

    Hydrogen bonds are important. There, that should be an sweepingly obvious enough statement to get things started. But they really are – hydrogen bonding accounts for the weird properties of water, for one thing, and it’s those weird properties that are keeping us alive. And leaving out the water (a mighty big step), internal hydrogen… Read More
  • Drug Industry History

    Jargon Will Save Us All

    Moore’s Law: number of semiconductors on a chip doubling every 18 months or so, etc. Everyone’s heard of it. But can we agree that anyone who uses it as a metaphor or perscription for drug research doesn’t know what they’re talking about? I first came across the comparison back during the genomics frenzy. One company… Read More
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