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Posts tagged with "In Silico"

  • In Silico

    Where’s the Best Place to Apply Modeling to Drug Discovery?

    An e-mail correspondent and I were discussing this question, and I thought it would be an interesting one for everyone. He’s a computational guy, and he’s been wondering where the best use of computation/modeling effort in drug research might be. The obvious place to apply it is in lead generation and SAR development – but… Read More
  • In Silico

    Foldit Notches a Protein Structure Success (And Some Failures)

    I wrote last year about Foldit, a collaborative effort to work on protein structure problems that’s been structured as an open-access game. Now the team is back with another report on how the project is going, and it’s interesting stuff. The headlines have generally taken the “Computer Gamers Solve Incredible Protein Problem That… Read More
  • In Silico

    Design a Molecule, Win an IPad (Which is More Than You Usually Get)

    For those of you who are (or have always wanting to try being) molecular modelers, Cresset Design is holding a contest you might enjoy. They’re putting up a molecule and giving out temporary licenses to their modeling software, and inviting people to come up with the closest bioisosteric match. The winner gets a free IPad2. Read More
  • In Silico

    Modeling and Structure

    Man, am I getting all kinds of comments (here and by e-mail) about my views on modeling, QSAR, and the like. I thought it might be helpful for me to clarify my position on these things. First off, structure. It’s a valuable thing to have. My comments on the recent Nature Reviews Drug Discovery article… Read More
  • Drug Development

    Value in Structure?

    A friend on the computational/structural side of the business sent along this article from Nature Reviews Drug Discovery. The authors are looking through the Thomson database at drug targets that are the subject of active research in the industry, and comparing the ones that have structural information available to the ones that don’t: enzyme… Read More
  • Biological News

    Maybe We Should Make It More of a Game

    David Baker’s lab at the University of Washington has been working on several approaches to protein structure problems. I mentioned Rosetta@home here, and now the team has published an interesting paper on another one of their efforts, FoldIt. That one, instead of being a large-scale passive computation effort, is more of an active process &# Read More
  • In Silico

    Free Software

    The folks at Cresset sent me a note about a free download of some software that they’ve developed for molecular fields (an approach you can read more about here). Fieldview is a free tool for trying this out yourself, and can be had here. Worth a look for the computationally curious, especially at the price. Read More
  • In Silico

    What Has Bioinformatics Ever Done For Us?

    A reader points me to this discussion, which is trying to figure out what the most useful discovery made via bioinfomatics is so far. There’s a $100 prize for the winning suggestion, just to keep the discussion moving (and no, I don’t anticipate offering cash bounties around here any time soon!) The early going seems… Read More
  • In Silico

    Modeling in Drug Discovery: Questions?

    I’ll have the opportunity to sit in on a few talks during a conference on free energy calculations in drug design. Since I’m not a computational guy myself, I’ll be picking my sessions carefully, but I am interested in hearing what the state of the art is. If we could just walk right up and… Read More
  • In Silico

    Unlovely Polyphenols

    Here’s a new paper from the folks at the Burnham Institute and UCSD on a new target for vaccinia virus. They’re going after a virulence factor (N1L) through computational screening, which is a challenge, since this is a protein-protein interaction. They pulled out a number of structures, which have some modest activity in cell infection… Read More
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