Pfizer using RosettaDock on the Amazon Cloud
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!!!!
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Thank you for the nice write up. The Gray lab definitely deserves credit for their excellent work on RosettaDock and RosettaAntibody! If space permitted I would have definitely mentioned them and the rest of the excellent Rosetta community. It should be noted we leverage EC2 for refinement only while the modeling and initial docking is done in-house, for now.
Cheers,
Adam
Full atom refinement is certainly one of the features that has set RosettaDock apart from other docking software but is (as you know!) computationally expensive. Many folks I have worked with like the combination of ZDOCK for global searching followed by RosettaDock for high resolution/full atom refinement.
On a different note, figuring out who has contributed what to Rosetta can be tricky (even for the developers
). I still think the best remedy is for each developer to add ‘please cite: Mole, Guaca, et al., Journal of Artificial Organisms, 2050′ directly to the output files of their modes (or sub-sub-modes), but most of the publications come long after the developer has moved on….
Thanks again for the article. It’s great for all of us to see Rosetta’s life outside of the ivory towers.
I like running Piper followed by Rosetta (Capri round 17, target 39?) (Piper available for download from htttp://cluspro.bu.edu soon).
I’ve thought that using Amazon DevPay to run EC2 instances for software would be an interesting concept for providing software to comapnies for some time, but been told that pharmaceuticals don’t like their data to leave the house, so I shuffled it away as an idea that was too early. That Pfizer is using EC2 provides some hope that maybe the pharmaceutical world would allow this.
Always like to see information on Cloud Computing! Looks like Australians are starting to wake up to it too with Telstra announcing a $500m spend this week on cloud computing services.