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Posts tagged with "In Silico"

  • 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
  • In Silico

    Mexican Lemons To the Rescue

    Thanks to a comment on this post, I’ve had a chance to read this interesting article from Stephen Johnson of Bristol-Myers Squibb, entitled “The Trouble with QSAR (Or How I Learned to Stop Worrying And Embrace Fallacy)”. (As a side note, it’s interesting to see that people still make references to the titling of Dr. Read More
  • Biological News

    The Motions of a Protein

    So, people like me spend their time trying to make small molecules that will bind to some target protein. So what happens, anyway, when a small molecule binds to a target protein? Right, right, it interacts with some site on the thing, hydrogen bonds, hydrophobic interactions, all that – but what really happens? That’s surprisingly… Read More
  • Drug Assays

    Structure-Activity: Lather, Rinse, and Repeat

    Medicinal chemists spend a lot of their time exploring and trying to make sense of structure-activity relationships (SARs). We vary our molecules in all kinds of ways, have the biologists run them through the assays, and then sit down to make sense of the results. And then, like as not, we get up again after… Read More
  • In Silico

    Floppiness Is Not Your Friend: Who Knew?

    There’s a trick that every medicinal chemist learns very early, and continues to apply every time its feasible: take two parts of your compound, and tie them together into a ring. The reason that works so well may not be immediately obvious if you’re not a medicinal chemist, so let me expand on them a… Read More
  • General Scientific News

    Protein Folding: Complexity to Make More Complexity?

    Want a hard problem? Something to really keep you challenged? Try protein folding. That’ll eat up all those spare computational cycles you have lounging around and come back to ask for more. And it’ll do the same for your brain cells, too, for that matter. The reason is that a protein of any reasonable size… Read More
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