Reproducing computational biology protocols is one of the difficult challenges facing computational biologists today. Often times, it is rarely feasible to replicate the computational environment of an original work because of the complexity of macromolecular modeling protocols. Moreover, much of this work is new research and not focused solely on the algorithms or workflows. As a result, published results often contain method descriptions with inconsistently stated protocols and dependencies.
In the new PLoS ONE Collection: RosettaCon 2010, over 15 academic groups from Rosetta Commons have attempted to capture these protocols in a sufficiently complete and formal way. This Collection aims to make several of the latest Rosetta macromolecular modeling protocols from the 2010 Rosetta Developers Meeting accessible to all.
Three main contributions came from the meeting and are represented in the PLoS ONE Collection.
1. New Rosetta applications: Several articles describe specific applications in biology or chemistry, including de novo enzyme design, modeling classes of protein loops, design of temperature sensitive mutations, and design of peptides to inhibit large surface area protein interactions.
2. Rosetta basic science: Several of the contributions in this Collection are Rosetta basic science papers of this type. Examples include: incorporation of non-canonical amino acids in Rosetta design, multi-state design, new Rosetta kinematics, new protein docking protocols, and anchored design. Each example has the full protocol that lead to the incorrect prediction fully described as well as the correct (“native”) structure; thus these protocols are key elements in defining and judging future improvement in Rosetta and other codes.
3. Rosetta code development: Multiple articles describe new code refactoring, extensions or improvements to the implementation of Rosetta. Several articles discuss the creation of multi-purpose high level interfaces to the components of Rosetta. Examples include an XML scripting interface for Rosetta, an interactive python interface to the Rosetta code, and an object oriented API for generating Rosetta fragments.
RosettaCon 2010 provides the larger community direct access to the exact protocols used in each of these papers. This construction was intended to allow other community members and Rosetta users to reproduce the work, allow competing groups to validate and improve upon the work, and finally, make it rapidly accessible to new users with similar biological applications.
It should be noted that this Collection is itself a social experiment and the collaborators wrestled with how best to capture an evolving set of processes in a way that does not overly burden authors, works across a distributed community without a central authority for methods capture, is timely, and is sufficiently self-consistent that readers will invest their time in the results.
The paper, 2010 Rosetta Developers Meeting: Macromolecular Prediction and Design Meets Reproducible Publishing, by Renfrew et al. was adapted to create this post.
Collection Citation: RosettaCon 2010 (2011) PLoS Collections: http://www.ploscollections.org/RosettaCon2010