/home/corante/public_html/pipeline/ en-us derekb.lowe@gmail.com 2012-01-26T07:31:12-05:00 hourly 1 2000-01-01T12:00+00:00 http://pipeline.corante.com/archives/2012/01/26/putting_a_number_on_chemical_beauty.php There's a new paper out in Nature Chemistry called "Quantifying the Chemical Beauty of Drugs". The authors are proposing a new "desirability score" for chemical structures in drug discovery, one that's an amalgam of physical and structural scores. To their... 75405@/home/corante/public_html/pipeline/ Life in the Drug Labs 2012-01-26T07:31:12-05:00 http://pipeline.corante.com/archives/2012/01/09/a_look_into_the_future.php For a look into a possible drug-discovery future (from the computational optimist viewpoint), you might want to check out a brief bit of science fiction, "Alpha Shock", in the Journal of Computer-Aided Molecular Design. Some excerpts to give you the... 75369@/home/corante/public_html/pipeline/ In Silico 2012-01-09T08:40:55-05:00 http://pipeline.corante.com/archives/2011/11/07/wheres_the_best_place_to_apply_modeling_to_drug_discovery.php 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.... 75263@/home/corante/public_html/pipeline/ In Silico 2011-11-07T13:10:40-05:00 http://pipeline.corante.com/archives/2011/09/20/foldit_notches_a_protein_structure_success_and_some_failures.php 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.... 75184@/home/corante/public_html/pipeline/ In Silico 2011-09-20T07:22:24-05:00 http://pipeline.corante.com/archives/2011/08/26/design_a_molecule_win_an_ipad_which_is_more_than_you_usually_get.php 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... 75153@/home/corante/public_html/pipeline/ In Silico 2011-08-26T07:03:59-05:00 http://pipeline.corante.com/archives/2011/03/29/modeling_and_structure.php 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... 74925@/home/corante/public_html/pipeline/ In Silico 2011-03-29T11:23:48-05:00 http://pipeline.corante.com/archives/2011/03/28/value_in_structure.php 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... 74923@/home/corante/public_html/pipeline/ In Silico 2011-03-28T06:20:32-05:00 http://pipeline.corante.com/archives/2010/08/09/maybe_we_should_make_it_more_of_a_game.php 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,... 74613@/home/corante/public_html/pipeline/ In Silico 2010-08-09T08:53:00-05:00 http://pipeline.corante.com/archives/2010/06/22/free_software.php 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... 74543@/home/corante/public_html/pipeline/ In Silico 2010-06-22T12:43:02-05:00 http://pipeline.corante.com/archives/2010/06/18/what_has_bioinformatics_ever_done_for_us.php 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,... 74536@/home/corante/public_html/pipeline/ In Silico 2010-06-18T06:31:55-05:00 http://pipeline.corante.com/archives/2010/05/17/modeling_in_drug_discovery_questions.php 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... 74472@/home/corante/public_html/pipeline/ In Silico 2010-05-17T06:32:43-05:00 http://pipeline.corante.com/archives/2010/05/10/unlovely_polyphenols.php 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.... 74461@/home/corante/public_html/pipeline/ Infectious Diseases 2010-05-10T10:20:47-05:00 http://pipeline.corante.com/archives/2010/05/10/bill_gates_put_some_money_on_schrodinger.php My take on the recent news that Bill Gates has invested ten million dollars in the computational drug design company Schrödinger is here at Nature News. (They've recently made all their stories open-access, by the way, so you don't need... 74460@/home/corante/public_html/pipeline/ In Silico 2010-05-10T07:52:20-05:00 http://pipeline.corante.com/archives/2010/05/04/another_proposal_for_the_scientific_literature.php I was talking with a colleague yesterday, and I suddenly had an insight into an opportunity in scientific publishing. We were discussing the various computational/modeling papers that you see out in the literature. Some of them are quite interesting, many... 74443@/home/corante/public_html/pipeline/ The Scientific Literature 2010-05-04T10:09:51-05:00 http://pipeline.corante.com/archives/2010/03/29/compounds_and_proteins.php For the medicinal chemists in the audience, I wanted to strongly recommend a new paper from a group at Roche. It's a tour through the various sorts of interactions between proteins and ligands, with copious examples, and it's a very... 74370@/home/corante/public_html/pipeline/ Drug Assays 2010-03-29T08:17:20-05:00