Macromolecular Modeling Blog ™

RosettaCon 2009 has ended just a few days ago.

This was a very exciting meeting, gathering almost all Rosetta developers from around the world, and representatives of the major industry licensees of Rosetta. The talks were quite diverse, ranging from new Rosetta protocols under development, applications with regards to numerous biological systems, and up to code architecture and future development of the code.

For scientists specializing in a specific field (such as computational structural biology – just off the top of my head) there are rare occasions in which meetings are dedicated entirely to their topic. This was such a conference! All through the three days of conference and one day of hiking, people had talked, discussed, brain stormed, ate, breathed, thought, swam, hiked, mingled and laughed protein structure. If the coffee break was drawn as a comic figure, with bubble clouds to depict thoughts and conversations, it would be a sea of alpha-helices, weird looking loops, rotamers, ligands and co-factors at interfaces, strange folds and stranger rainbow colored cartoon proteins. A modeler’s utopia.

All along the meeting two trends kept emerging again and again, one from the scientific end, and the other, literally, at the user end.

From the scientific point of view: It seems that the bar has been raised. Where a couple of years ago, structural predictions of within 2A were considered a success for protocols such as loop modeling, ligand docking and interface designs (These protocols do not include ab-initio structure prediction, and protein-protein docking, although those fields have also developed greatly) now, a more stringent criterion of 1A is becoming a common measure of success. Such figures of successful predictions or designs were seen in many talks and a 1A criterion for benchmarking was prevalent. High-resolution modeling is not a new phenomenon, but it seems that it’s now becoming main-stream.

From the user end: Those of you who ever tried to run Rosetta, must know it is not designed for user expirience. The command line syntax and elaborate options system are great for the expert developer and for large scale scripting and benchmarking, but introduce a steep learning curve for the untrained Rosetta user. It seems that this challenge was also met. Many new interfaces have become available for Rosetta and are being actively developed and supported. Starting from PyRosetta which is a python binding around Rosetta code that allows the user to run Rosetta either through python scripts or through an interactive python interpreter. Going through the “RosettaScripts” module, released in the last version, that allows the user to create novel protocols in Rosetta, drawing from its wide, established tool box, without any need of actual programming or compiling. And ending, with plans for a much anticipated “FoldIt” like GUI to Rosetta that would allow real time manipulation of your biological system in a very simple, elegant and visually stimulating user interface.

I was really impressed by the advancements achieved by this community and was proud to be a part of it. I want to thank all the participants, presenters, developers, industry representatives and especially the organizers Dr. Ora Schueler-Furman and Dr. Phil Bradley for this wonderful meeting, and I hope to see all of you again next year.

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