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Posts tagged with "In Silico"

  • Drug Assays

    Lilly’s Virtual Med-Chem Assistant

    Here’s an interesting new paper from Lilly (brought to my attention by Ash Jogalekar on Twitter). “Creating a virtual assistant for medicinal chemistry” is the title, but fear not: this is not something that’s come to elbow you aside at the bench. Well, not yet. What they’re talking about is a software agent that is… Read More
  • Chemical News

    The Cyclofluidic Story

    The recent post here on automation in chemistry (especially medicinal chemistry) is a good intro for this paper in ACS Med. Chem. Letters. It’s from David Parry, who led Cyclofluidic, and I’ve blogged about them a few times over the years. That was a company formed in 2008 in the UK to try to develop… Read More
  • Biological News

    Antibody Design, Publicly Challenged

    Comes now some rather disturbing news in the antibody field. These things are extremely important, both as therapeutics and as research reagents, and developing them for either purpose is no stroll down the garden walk. There are a number of techniques for raising and producing antibodies (see that first link), but they all have their… Read More
  • In Silico

    An Intro to Deep Learning

    I wanted to mention a timely new book, Deep Learning for the Life Sciences, that I’ve received a copy of. It’s by Bharath Ramsundar at Computable, Peter Eastman at Stanford, Pat Walters at Relay, and Vijay Pande at Andreessen Horowitz, and I’ve been using it to shore up my knowledge in this area. From what… Read More
  • In Silico

    Farewell to “Watson For Drug Discovery”

    STAT is reporting that IBM has stopped trying to sell their “Watson for Drug Discovery” machine learning/AI tool, according to sources within the company. I have no reason to doubt that – in fact, I’ve sort of been expecting it. But no one seems to have told IBM’s website programming team, because the pages touting… Read More
  • Drug Assays

    Comparing Compound Collections

    A common question – well, it should be a common question, anyway – is “How do I make sure that this compound collection is a useful one to screen?” There are alternative forms that come down to the same issues – if you’re putting together a new focused screening set, what should be in it?… Read More
  • Analytical Chemistry

    A Close Look at Fragments

    Here’s a look from the D. E. Shaw research team at fragment binding, and even if you don’t do fragment-based drug discovery, it’s worth a read. That’s because the mechanisms by which fragments bind to proteins are most likely the fundamental ones by which larger molecules bind as well; this is the reductionist look at… Read More
  • Chemical News

    Predicting – Or Not Predicting – New Materials

    We chemists would love to be able to do just a tiny bit less chemistry now and then and just let models and simulations tell us what would happen instead. Only every once in a while – you wouldn’t want to obtain such a perfectly accurate picture of chemical and physical interactions that there was… Read More
  • Drug Assays

    Virtual Screening – As Big As It Currently Gets

    This new paper on “ultra-large” virtual screening is well worth a look in detail. We find a great many lead compounds in this business by random screening of compound libraries, and virtual screening is (as the name implies) the technique of doing this computationally instead of with hundreds (thousands) of sample plates and tireless ro… Read More
  • In Silico

    The Latest on Protein Folding

    The results of the biannual CASP (Critical Assessment of Structure Prediction) effort have been released. This is a widely-watched competition between different groups (and different programs, methods, hardware, etc.) to see how well protein structures can be predicted de novo from just the protein sequences themselves. In the main category, the or… Read More
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