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Posts tagged with "In Silico"

  • In Silico

    Modeling in Drug Discovery: Questions?

    I’ll have the opportunity to sit in on a few talks during a conference on free energy calculations in drug design. Since I’m not a computational guy myself, I’ll be picking my sessions carefully, but I am interested in hearing what the state of the art is. If we could just walk right up and… Read More
  • In Silico

    Unlovely Polyphenols

    Here’s a new paper from the folks at the Burnham Institute and UCSD on a new target for vaccinia virus. They’re going after a virulence factor (N1L) through computational screening, which is a challenge, since this is a protein-protein interaction. They pulled out a number of structures, which have some modest activity in cell infection… Read More
  • In Silico

    Bill Gates Put Some Money On Schrödinger

    My take on the recent news that Bill Gates has invested ten million dollars in the computational drug design company Schrödinger is here at Nature News. (They’ve recently made all their stories open-access, by the way, so you don’t need a subscription to get the full stories). In short, I think that patient billionaire money… Read More
  • In Silico

    Another Proposal For the Scientific Literature

    I was talking with a colleague yesterday, and I suddenly had an insight into an opportunity in scientific publishing. We were discussing the various computational/modeling papers that you see out in the literature. Some of them are quite interesting, many are worth looking at if it’s your particular field – but many others are, well… Read More
  • Drug Assays

    Compounds and Proteins

    For the medicinal chemists in the audience, I wanted to strongly recommend a new paper from a group at Roche. It’s a tour through the various sorts of interactions between proteins and ligands, with copious examples, and it’s a very sensible look at the subject. It covers a number of topics that have been discussed… Read More
  • Drug Assays

    We Don’t Know Beans About Biotin

    You know, you’d think that we’d understand the way things bind to proteins well enough to be able to explain why biotin sticks so very, very tightly to avidins. That’s one of the most impressive binding events in all of biology, short of pushing electrons and forming a solid chemical bond – biotin’s stuck in… Read More
  • 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