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Posts tagged with "In Silico"

  • Analytical Chemistry

    The 3D Fragment Consortium

    Fragment-based screening comes up here fairly often (and if you’re interested in the field, you should also have Practical Fragments on your reading list). One of the complaints both inside and outside the fragment world is that there are a lot of primary hits that fall into flat/aromatic chemical space (I know that those two… Read More
  • Chemical Biology

    Evolving Enzymes: Let ‘Em Rip

    Evolutionary and genetic processes fascinate many organic chemists, and with good reason. They’ve provided us with the greatest set of chemical catalysts we know of: enzymes, which are a working example of molecular-level nanotechnology, right in front of us. A billion years of random tinkering have accomplished a great deal, but (being human… Read More
  • Drug Assays

    More Whitesides on Ligand Binding

    George Whitesides and his lab have another paper out on the details of how ligands bind to proteins. They’re still using the favorite model enzyme of all time (carbonic anhydrase), the fruit fly and nematode of the protein world. Last time around, using a series of ligands and their analogs with an extra phenyl in… Read More
  • In Silico

    MedChemica: When One Compound Collection Isn’t Enough

    According to SciBx, here’s another crack at computational solutions for drug discovery: MedChemica, a venture started by several ex-AstraZeneca scientists. They’re going to be working with data from both AZ and Roche, using what sounds like a “matched molecular pair” approach: Although other algorithms try to relate structur… Read More
  • Analytical Chemistry

    GPCRs Are As Crazy As You Thought

    That’s my take-away from this paper, which takes a deep look at a reconstituted beta-adrenergic receptor via fluorine NMR. There are at least four distinct states (two inactive ones, the active one, and an intermediate), and the relationships between them are different with every type of ligand that comes in. Even the ones that look… Read More
  • Biological News

    How Many Binding Pockets Are There?

    Just how many different small-molecule binding sites are there? That’s the subject of this new paper in PNAS, from Jeffrey Skolnick and Mu Gao at Georgia Tech, which several people have sent along to me in the last couple of days. This question has a lot of bearing on questions of protein evolution. The paper’s… Read More
  • In Silico

    IBM’s Watson Does Drug Discovery?

    I saw this story this morning, about IBM looking for more markets for its Watson information-sifting system (the one that performed so publicly on “Jeopardy”. And this caught my eye for sure: John Baldoni, senior vice president for technology and science at GlaxoSmithKline, got in touch with I.B.M. shortly after watching Watson’s “J… Read More
  • Drug Assays

    All Those Drug-Likeness Papers: A Bit Too Neat to be True?

    There’s a fascinating paper out on the concept of “drug-likeness” that I think every medicinal chemist should have a look at. It would be hard to count the number of publications on this topic over the last ten years or so, but what if we’ve been kidding ourselves about some of the main points? The… Read More
  • 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