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Posts tagged with "In Silico"

  • Drug Assays

    A New Way to Estimate a Compound’s Chances?

    Just a few days ago we were talking about whether anything could be predicted about a molecule’s toxicity by looking over its biophysical properties. Some have said yes, this is possible (that less polar compounds tend to be more toxic), but a recent paper has said no, that no such correlation exists. This is part… Read More
  • Drug Assays

    We Can’t Calculate Our Way Out of This One

    Clinical trial failure rates are killing us in this industry. I don’t think there’s much disagreement on that – between the drugs that just didn’t work (wrong target, wrong idea) and the ones that turn out to have unexpected safety problems, we incinerate a lot of money. An earlier, cheaper read on either of those… Read More
  • In Silico

    Chemical Space

    I’m listening to Jean-Louis Reymond of Bern talking about the GDB data set, the massive enumerated set of possible molecules. That’s the set of chemically feasible molecules at or below a certain heavy atom count – the first iteration was GDB11 (blogged about here), and it’s since been extended to GDB13, which has nearly one… Read More
  • Clinical Trials

    The Virtual Clinical Trial: Not Quite Around the Corner

    Here’s one of those “Drug Discovery of. . .the. . .Future-ure-ure-ure” articles in the popular press. (I need a reverb chamber to make that work property). At The Atlantic, they’re talking with “medical futurists” and coming up with this: The idea is to combine big data and computer simulations—the kind an engi… Read More
  • Drug Assays

    Hosed-Up X-Ray Structures: A Big Problem

    X-ray crystallography is great stuff, no doubt about it. But it’s not magic. It takes substantial human input to give a useful structure of a ligand bound to a protein – there are decisions to be made and differences to be split. It’s important to emphasize, for those of us who are not crystallographers, that… Read More
  • Drug Assays

    Predicting New Targets – Another Approach

    So you make a new chemical structure as part of a drug research program. What’s it going to hit when it goes into an animal? That question is a good indicator of the divide between the general public and actual chemists and pharmacologists. People without any med-chem background tend to think that we can predict… Read More
  • Drug Industry History

    Ancient Modeling

    I really got a kick out of this picture that Wavefunction put up on Twitter last night. It’s from a 1981 article in Fortune, and you’ll just have to see the quality of the computer graphics to really appreciate it. That sort of thing has hurt computer-aided drug design a vast amount over the years. Read More
  • Drug Development

    Predicting What Group to Put On Next

    Here’s a new paper in J. Med. Chem. on software that tries to implement matched-molecular-pair type analysis. The goal is a recommendation – what R group should I put on next? Now, any such approach is going to have to deal with this paper from Abbott in 2008. In that one, an analysis of 84,000… Read More
  • In Silico

    Computational Nirvana

    Wavefunction has a post about this paper from J. Med. Chem. on a series of possible antitrypanosomals from the Broad Institute’s compound collection. It’s a good illustration of the power of internal hydrogen bonds – in this case, one series of isomers can make the bond, but that ties up their polar groups, making them… Read More
  • Drug Assays

    Ligand Efficiency: A Response to Shultz

    I’d like to throw a few more logs on the ligand efficiency fire. Chuck Reynolds of J&J (author of several papers on the subject, as aficionados know) left a comment to an earlier post that I think needs some wider exposure. I’ve added links to the references: An article by Shultz was highlighted earlier in… Read More
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