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Posts tagged with "In Silico"

  • In Silico

    Melting Keys and Squishy Locks

    Pretty much the only thing that an interested lay person has heard about ligand binding is the “lock and key” metaphor. I’m not saying that you could walk down the sidewalk getting nods of recognition with it, but if someone’s heard anything about how enzymes or receptors work (well, anything correct), that’s probably… Read More
  • Drug Assays

    No Shortcuts

    I wanted to link tonight to the “Milkshake Manifesto” over at OrgPrep Daily. It’s a set of rules for med-chem, and looking them over, I agree with them pretty much across the board. There’s a general theme in them of getting as close to the real system as you can, which is a theme I’ve… Read More
  • In Silico

    Wrong, But Still Convincing

    SciTheory has a post, complete with links to the relevant articles in Science, etc., on a recent batch of trouble in structural biology. Geoffrey Chang and his group at Scripps have been working on the structures of transporter proteins, which sit in the cell membrane and actively move nonpermeable molecules in and out. There are… Read More
  • In Silico

    Love and Anger

    Glenn Reynolds gave the pharma industry a much-appreciated thank-you card over at Instapundit: Only a moron would want to live in a society where people are ashamed to work for drug companies. And yet, I’m not surprised to see that resulting from the demagogy that abounds among politicians and “public interest” types who are not… Read More
  • In Silico

    Enzymes Do Whatever They Want To

    It’s been a while since I wrote about the neuraminidase inhibitors (Tamiflu and Relenza, oseltamavir and zanamivir). As we start to head into fall, though, I’m sure that avian flu will invade the headlines again, if nothing else (and I hope it’s nothing else). There’s an interesting report in Nature (subscriber link) on how… Read More
  • In Silico

    Crystals of Doubt

    Here’s a limits-to-knowledge post for you. On Wednesday, when I was cranking out a batch of an intermediate we’re using these days, I needed to separate two fairly closely related compounds (which I’ll call A and B) from each other. One surefire way to have done that was chromatography, but I just didn’t have time… Read More
  • In Silico

    Molecular Modeling Cage Match

    I mentioned an interesting paper that’s coming out in the Journal of Medicinal Chemistry on molecular modeling. It’s a long one from a large group of people scattered across GlaxoSmithKline’s worldwide research facilities, entitled “A Critical Assessment of Docking Programs and Scoring Functions.” And that’s what… Read More
  • In Silico

    The Hazards of Molecular Modeling

    A comment to the last post really gave me the shivers: “I like to think of modelling as the “silent killer”. It is easy to rely on it for quick answers, and easy to forget that there is no substitute for an actual experiment. . . I remember asking a fellow scientist if a particular… Read More
  • In Silico

    Clamping Down, or Loosening Up?

    We medicinal chemists spend our days trying to make small molecules that bind to targets in living systems. Almost all of those targets are proteins of one sort or another, and most of them have binding pockets already built into them, which we’re trying to hijack for our own purposes. Molecular modelers try to figure… Read More
  • In Silico

    Crossing Your Fingers, Authoritatively

    I recall a project earlier in my career where we’d all been beating on the same molecular series for quite a while. Many regions of the molecule had been explored, and my urge was often to leave the reservation. I put some time into extending the areas we knew about, but I wanted to go… Read More
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