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Posts tagged with "In Silico"

  • Biological News

    Farewell to Bioinformatics

    Here are some angry views that I don’t necessarily endorse, but I can’t say that they’re completely wrong, either. A programmer bids an angry farewell to the bioinformatics world: Bioinformatics is an attempt to make molecular biology relevant to reality. All the molecular biologists, devoid of skills beyond those of a laboratory… Read More
  • "Me Too" Drugs

    The Hydrophobic Effect: I Don’t Understand It, Either

    We medicinal chemists talk a good game when it comes to the the hydrophobic effect. It’s the way that non-water-soluble molecules (or parts of molecules) like to associate with each other, right? Sure thing. And it works because of. . .well, van der Waals forces. Or displacement of water molecules from protein surfaces. Or entropic… Read More
  • Chemical Biology

    Halogen Bonds

    Here’s a recent paper in J. Med. Chem. on halogen bonding in medicinal chemistry. I find the topic interesting, because it’s an effect that certainly appears to be real, but is rarely (if ever) exploited in any kind of systematic way. Halogens, especially the lighter fluorine and chlorine, are widely used substituents in medicinal chemi… Read More
  • In Silico

    Virtual Screening, The Good Parts and the Bad Ones

    Virtual screening is what many people outside the field are thinking of when they talk about the use of computational models in drug discovery. There are many other places where modeling can pitch in, but one of the dreams has always been to take a given protein target and a long list of chemical structures… Read More
  • Drug Assays

    Automated Ligand Design?

    There’s a paper out in Nature with the provocative title of “Automated Design of Ligands to Polypharmcological Profiles”. Admittedly, to someone outside my own field of medicinal chemistry, that probably sounds about as dry as the Atacama desert, but it got my attention. It’s a large multi-center contribution, but the princi… Read More
  • In Silico

    Did Kaggle Predict Drug Candidate Activities? Or Not?

    I notied this piece on Slate (originally published in New Scientist) about Kaggle, a company that’s working on data-prediction algorithms. Actually, it might be more accurate to say that they’re asking other people to work on data-prediction algorithems, since they structure their tasks as a series of open challenges, inviting all comer… Read More
  • Chemical News

    Chemistry Software Questions Here

    As mentioned the other day, this will be a post for people to ask questions directly to Philip Skinner (SDBioBrit) of Perkin-Elmer/Cambridgesoft. He’s doing technical support for ChemDraw, ChemDraw4Excel, E-Notebook, Inventory, Registration, Spotfire, Chem3D, etc., and will be monitoring the comments and posting there. Hope it helps some peop… Read More
  • Drug Assays

    Watch that Little Letter “c”

    Hang around a bunch of medicinal chemists (no, really, it’s more fun than you’d think) and you’re bound to hear discussion of cLogP. For the chemists in the crowd, I should warn you that I’m about to say nasty things about it. For the nonchemists in the crowd, logP is a measure of how greasy… Read More
  • Drug Development

    Predicting Toxicology

    One of the major worries during a clinical trial is toxicity, naturally. There are thousands of reasons a compound might cause problem, and you can be sure that we don’t have a good handle on most of them. We screen for what we know about (such as hERG channels for cardiovascular trouble), and we watch… Read More
  • Drug Assays

    The Artificial Intelligence Economy?

    Now here’s something that might be about to remake the economy, or (on the other robotic hand) it might not be ready to just yet. And it might be able to help us out in drug R&D, or it might turn out to be mostly beside the point. What the heck am I talking about… Read More