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Posts tagged with "In Silico"

  • In Silico

    Computational Nirvana

    Wavefunction has a post about this paper from J. Med. Chem. on a series of possible antitrypanosomals from the Broad Institute’s compound collection. It’s a good illustration of the power of internal hydrogen bonds – in this case, one series of isomers can make the bond, but that ties up their polar groups, making them… Read More
  • Drug Assays

    Ligand Efficiency: A Response to Shultz

    I’d like to throw a few more logs on the ligand efficiency fire. Chuck Reynolds of J&J (author of several papers on the subject, as aficionados know) left a comment to an earlier post that I think needs some wider exposure. I’ve added links to the references: An article by Shultz was highlighted earlier in… Read More
  • Biological News

    “It Is Not Hard to Peddle Incoherent Math to Biologists”

    Here’s a nasty fight going on in molecular biology/bioinformatics. Lior Pachter of Berkeley describes some severe objections he has to published work from the lab of Manolis Kellis at MIT. (His two previous posts on these issues are here and here). I’m going to use a phrase that Pachter hears too often and say that… Read More
  • In Silico

    A New Metabolism Predictor

    Drug metabolism is a perennial topic for us small-molecule people. Watching your lovingly optimized molecules go through the shredding-machine of the liver is an instructive experience, not least when you consider how hard it would be for you to do some of the chemistry that it does. (For reference and getting up to speed on… Read More
  • In Silico

    Picking Diverse Compounds

    Diversity deck, diversity set, diversity collection: most chemical screening efforts try to have some bunch of compounds that are selected for being as unlike each other as possible. Fragment-based collections, being smaller by design, are particularly combed through for this property, in order to cover the most chemical space possible. But how, ex… Read More
  • In Silico

    Standards of Proof

    Here are some slides from Anthony Nicholls of OpenEye, from his recent presentation here in Cambridge on his problems with molecular dynamics calcuations. Here’s his cri du coeur (note: fixed a French typo from the original post there): . . .as a technique MD has many attractive attributes that have nothing to do with its… Read More
  • Chemical News

    Low Energy Records

    Pick an empirical formula. Now, what’s the most stable compound that fits it? Not an easy question, for sure, and it’s the topic of this paper in Angewandte Chemie. Most chemists will immediately realize that the first problem is the sheer number of possibilities, and the second one is figuring out their energies. A nonscientist… Read More
  • In Silico

    When the “c” in cLogP Stands For “Crazy” (Update: Fixed!)

    I don’t know how many readers out there use the cLogP function in ChemDraw, but you might want to take a look at the illustration here before you use it again. A reader alerted me to this glitch: drawing in explicit hydrogens sends it into an even stranger world of fantasy than most calculated logP… Read More
  • In Silico

    Models and Reality

    I have to admit that I enjoyed seeing this question asked: how come we still use wind tunnels in aerodynamic engineering? Why don’t we just model everything in software? The answers, from people who’ve actually done some of the work, are what you might expect: the models all involve degrees of approximation, gloss over some… Read More
  • Drug Assays

    Unraveling An Off-Rate

    Medicinal chemists talk a lot more about residence time and off rate than they used to. It’s become clear that (at least in some cases) a key part of a drug’s action is its kinetic behavior, specifically how quickly it leaves its binding site. You’d think that this would correlate well with its potency, but… Read More