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Posts tagged with "In Silico"

  • 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
  • In Silico

    Using the Same FEP Ruler

    With free energy perturbation having its time in the calculational spotlight, thanks to Schrödinger and others, it seems worthwhile to link to this new paper. It’s a proposal for a common framework to analyze the results of such work. That’s needed, because (as far as I can tell, as a definite outsider) every group seems… Read More
  • Clinical Trials

    Levels of Data

    Here’s a brief article in Science that a lot of us should keep a copy of. Plenty of journalists and investors should do the same. It’s a summary of what sort of questions get asked of data sets, and the differences between them. There are six broad data analysis categories: 1. Descriptive. This is the… Read More
  • In Silico

    Sanofi Bets on Schrödinger

    Sanofi has signed an expanded deal with Schrödinger, the computational chemistry folks. Here’s something from the press release: Schrödinger has made a number of key scientific breakthroughs in recent years in the areas of protein and ligand structure determination and potency prediction that promise to have a transformative impact on the d… Read More
  • Biological News

    A Couple of Ycombinator’s Startups

    Last year I mentioned reports that the startup incubator Ycombinator was thinking of getting into the biopharma field. Here’s a look at the current crop of potential companies. One thing that stands out is that most of these seem to be focused on patient care or some sort of diagnostic. One exception is 20n, which… Read More
  • Chemical News

    Not Even Wrong

    This paper is not going to make a lot of computational chemists very happy at all. It’s from Dan Singleton and Erik Plata at Texas A&M, and it’s on the Morita-Bayliss-Hillman reaction. More specifically, though, it’s on the many computational attempts to decide on the mechanism of the MBH reaction, and taken together, they… Read More
  • In Silico

    Diversity and Similarity Scoring: Does One Size Ever Fit All?

    We spend a lot of time talking about compound similarities in this business. All those schemes for virtual screening, to find new activities for old compounds, to predict side effects and general toxicity, and many others besides rely on some sort of measurement of how similar various compounds (and collections of compounds) are to each… Read More
  • In Silico

    Neural Networks for Drug Discovery: A Work in Progress

    There have been many attempts over the years to bring together large amounts of biological and drug activity data, winnow them computationally, and come up with insights that would not be obvious to human eyes. It’s a natural thing to imagine – there are so many drug targets in the body, doing so many things… Read More
  • In Silico

    Is FEP Ready For the World?

    Here’s a paper that basically throws down the computational gauntlet. A large group of authors from Schrödinger, Nimbus, Columbia, Yale, and UC-Irvine say that their implementation of free energy perturbation (FEP) calculations really does lead to a significant number of more active compounds being predicted. That’s as compared to othe… Read More
  • Drug Assays

    The Old Binding Mode Switcheroo

    When a medicinal chemist gets a promising lead compound, the first thing that’s done to it is to start making modifications to the structure. Add methyls or fluorines, take some of the substituents back off, switch stereochemistry, switch carbons and nitrogens around, that sort of thing. And there you start to build up a structure-activity… Read More