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PhD position in Statistical Protein Structure Prediction, Copenhagen, Denmark

One of the major unsolved problems in bioinformatics is the protein folding problem: given an amino acid sequence, predict the overall three-dimensional structure of the corresponding protein. It has been known since the seminal work of Christian B. Anfinsen in the early seventies that the sequence of a protein encodes its structure, but the exact […]

Postdoctoral Position in Computational Bioengineering (Rice University)

The Kavraki group at Rice University is looking to hire an enthusiastic postdoctoral researcher to enhance their research efforts in computational structural biology, drug design, and computational bioengineering. The group has significant expertise in the development of methods for motion planning for complex systems in robotics. Their Open Motion Planning Library (OMPL, http://ompl.kavrakilab.org) is now […]

Nobel Prize Quips at PDBe

I received this email today from Gary Battle at PDBe . Very cool:   Nobel Prize Quips: Explore the structure of B2AR bound to its G-protein. Today, Nobel Laureates Robert J. Lefkowitz and Brian K. Kobilka take center stage in Stockholm where they will receive their Nobel Prize Medals for their studies of G-protein–coupled receptors […]

Postdocs in Genome-Scale Proteomics, Imaging-based Screening and Cancer Biology

  Three postdocs positions available at a great lab in Denmark. Read on:   We are seeking three Postdoctoral Fellows to The Cellular Signal Integration Group (C-SIG). The group is a network biology research group located at the Department of Systems Biology at the Technical University of Denmark (DTU). Our department represents one of the […]

Repost: a very loose and circular association to Pi Day

(Originally published March 14, 2009) Happy Pi (π) Day! Americans write dates in the MM/DD/YYYY format instead of the DD/MM/YYYY format used by the rest of the world.  Usually a rather painful and confusing format if you did not grow up with it, causing checks to bounce and leases to expire for those who recently […]

A new life form? Not so fast

So everybody is excited about the new GFAJ-1 bacterium that Felisa Wolfe-Simon and her colleagues have discovered. A common buzzphrase diffusing through the media and blogosphere is “NASA discovers a new  life form“. (Or, better yet alien life.) Big press conference, and I just finished going through  the article that Wolfe-Simon and colleagues have published in Science. Great […]

Carnival of Evolution #29

Yes, it’s that time when we all get together in front of the screen to watch another beautiful game played by that fantastic team contributing to the Carnival of Evolution. This time hosted on the lovely green pitch of Byte Size Biology. So get your popcorn, sunflower-seeds, crisps or any other culturally-appropriate sports-watching food and…… […]

Lake Arrowhead Microbial Genomics Conference

Quick post: at the Lake Arrowhead Microbial Genomics Conference. I’m a bad microblogger, but thankfully Jonathan Eisen and Ruchira Datta are doing a great job of covering this conference live. There is a friendfeed room. The Twitter hashtag is #LAMG10.  The science, people, food and location are all great. My student, David Ream, is presenting […]

Protein function, promiscuity, moonlighting and philosophy

I recently received an email from a graduate student in Philosophy regarding protein function. Not sure if that person wants his name advertised, so I will keep it to myself. “I am a fan of your blog, and interested in the philosophy of biology. One particularly interesting question is what makes something have a function; […]

Computational Bridge to Experiments

A bit of background information: this is a meeting I am really happy to be part of, and even more so honored to be a co-organizer. One of my main scientific interests is the prediction of the function of genes and proteins of unknown function. Some background information: we have sequenced more than 1000 genomes […]

Paweł Szczęsny in TEDx Warsaw

Pawel on Open Science. Full disclosure: I consider sharing an office with this guy for over a year to be one of the best experiences of my postdoc.

“Codon” is now a four letter word

As part of the process of manufacturing  a new car,  the designers will take the blueprints to the factory floor. There they will set up an experimental assembly line, tinkering with the manufacturing process of the prototype until it is ready for mass-production. Can we do the same with the machinery of life — the assembly […]

The polypharmacome

Pharmaceutical companies are always on the lookout for secondary drug targets. After all, if you invest billions developing a single drug, you would be more than happy to sell it as a treatment for two, three, or more different ailments. Sildenafil citrate was developed to treat angina and hypertension, but during phase I clinical trials, […]

Fold.it: wasting time in a good cause

I just spent the better part of a Saturday playing with Foldit. Foldit is an ongoing experiment in finding protein structures by harnessing the power of the mob – or gamers, as is the case here. The player is presented with a backbone & sidechain configuration, with the secondary structures mostly pre-determined. The problem is […]


The University of Alabama at Birmingham issued a statement last week asking that 11 structures be removed from the Protein Data Bank, as they are quite possibly fabricated. Wow. Very little detail was given by UAB’s statement (below), or by the media. Apparently all the structures are tied to one person, HMK Murthy, who could […]