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Posts tagged with "In Silico"

  • Chemical News

    The Algorithms Are Coming

    I think that every synthetic organic chemist should take a look at this paper in Angewandte Chemie. It’s on the application of computer algorithms to planning synthetic routes, which is a subject that’s been worked on for fifty years or more – without, it has to be said, making too much of an impression on… Read More
  • Drug Assays

    More Binding Sites Than Are Dreamt of in Your Philosophy

    Cryptic binding sites: now there’s a puzzle for you. When you look at a protein structure, even if you know nothing about its function, you can usually spot small-molecule binding sites without too much trouble. They tend to be pocket-like folds, often with particular polar motifs. (If the protein is an enzyme, the binding site/active… Read More
  • Animal Testing

    A Terrific Paper on the Problems in Drug Discovery

    Here’s a really interesting paper from consultants Jack Scannell and Jim Bosley in PLoS ONE, on the productivity crisis in drug discovery. Several things distinguish it: for one, it’s not just another “whither the drug industry” think piece, of which we have plenty already. This one get quantitative, attempting to figure out… Read More
  • Drug Assays

    Clouding Biology: That Verb Cuts Both Ways

    Here’s Steve Dickman at Forbes with a look at “cloud biology” approaches to medicine and drug discovery. This is an area I’ve written about several times before, and I also recommend Wavefunction’s take on this. I particularly like the quote from Mark Murcko about having to extrapolate from biology that’s “ Read More
  • Chemical News

    One Step Beyond! Maybe More.

    There are plenty of useful drugs whose structures are, well, odd-looking. Antibiotics, as a class, have a lot of these: macrocycles, polyenes, polyhydroxylated beasts that don’t fit in with a medicinal chemist’s ideas of what a reasonable compound should look like. The “Rule of Five” metrics have been debated endlessly for w… Read More
  • Drug Assays

    Pattern-Matching Binding Sites

    Here’s a recent paper that bears on the “How many binding pockets are there” question. Or maybe that’s the “How many different types of binding pockets” question, which last came up around here a couple of years ago. That one was a computational approach that suggested that there were around 500 different varieti… Read More
  • Drug Assays

    Not Quite There Yet

    I’ve been meaning to blog about this paper, because its abstract certainly promises a lot: . . .Target prediction software based on machine learning models correctly identified additional macromolecular targets of the computationally designed compound and the structurally related marketed drug azosemide. The study validates computational de n… Read More
  • Cancer

    Artificial Intelligence, You Say?

    Here’s a story from the Telegraph about a small company (Berg Pharmaceuticals), whose headline certainly got my attention: “Cancer drug development time halved thanks to artificial intelligence”. That set off some alarm bells for me, and not because I fear being replaced by a bearded AI quoting mispronounced Latin tags and John Cl… Read More
  • Drug Development

    Modeling the Rats, Who Model the Humans

    When you get down to it, one of the biggest problems in drug discovery is that there is (in most cases) no alternative but doing things the hard way. If you want to find out if your drug is going to work for a given disease, there’s no other way to be sure than to… Read More
  • Biological News

    Artificial Intelligence For Biology?

    A new paper in PLoS Computational Biology is getting a lot of attention (which event, while not trying to be snarky about it, is not something that happens every day). Here’s the press release, which I can guarantee that most of the articles written about this work will be based on. That’s because the paper… Read More