Macromolecular Modeling Blog ™

Roland Dunbrack shows off the capabilities of SCWRL4, the new version of his famous side chain prediction software. Indeed it seems that the new version has come a long way, especially in the form of a new, smoother backbone-dependent rotamer library. Roland promises to answer any questions regarding the new rotamer library, SCWRL, and also random questions.

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I’m happy to cross-post another elegant piece written by the MD specialist Bosco Ho. In this post Bosco compares the performance of Molecular Dynamics simulations with Monte Carlo simulations in reconstructing NMR S order parameters for microsecond biological processes. Curious to know which is better ?

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In a post yesterday on the Bleeding Edge Biotech Blog, Adam Kraut gives an expanded version of his article for Bio-IT World entitled Antibody Docking on the Amazon Cloud describing how Pfizer is leveraging the power and flexibility of cloud computing to run antibody docking simulations using Rosetta. Pfizer employed BioTeam (which Kraut consults for) to port Rosetta to the cloud. This is a fascinating article and certainly the Pfizer/BioTeam/Rosetta/Amazon synergy is a phenomenon on the bleeding edge.

I would add to the article that Jeffrey Gray at Johns Hopkins University was the lead developer of RosettaDock and RosettaAntibody. Rosetta has become synonymous with David Baker (and for good reason), but it is important to acknowledge continuing contributions to Rosetta outside of the Baker lab. Scientific collaborations can dissolve quickly when recognition is unevenly distributed, whether internally or as a result of outside perceptions (i.e. not as the result of any intentions by researchers in the collaboration).

If you use or write about Rosetta, please help us keep this unique collaboration going by acknowledging and citing the individual developers and researchers and their current labs!!!!

Next week, RDG will be teaching a three day course at the Center of Information Technology of the National Institutes of Health:

#468 Rosetta Hands-On Workshop

Are wikis the future of scientific collaboration in biology? 

The tremendous success of Wikipedia has raised the possibility of using wiki technology for scientific collaboration. However, it is not yet clear if traditional scientific methods can be acceptably incorporated into the ‘wiki’ paradigm. Despite this uncertainty, many tens of ‘scientific-wikis’ currently exist [1], with many more ‘annotation-wikis’ on the horizon. In this post we will discuss two key scientific concepts, and try to assess how they fit (or not) within the ‘wiki’ model. By Dan Bolser and Jong Bhak  (more…)