Abstract
The Rosetta molecular modeling software package provides experimentally tested and rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, nucleic acids, and a growing number of non-natural polymers. Despite its free availability to academic users and improving documentation, use of Rosetta has largely remained confined to developers and their immediate collaborators due to the code’s difficulty of use, the requirement for large computational resources, and the unavailability of servers for most of the Rosetta applications. Here, we present a unified web framework for Rosetta applications called ROSIE (Rosetta Online Server that Includes Everyone). ROSIE provides (a) a common user interface for Rosetta protocols, (b) a stable application programming interface for developers to add additional protocols, (c) a flexible back-end to allow leveraging of computer cluster resources shared by RosettaCommons member institutions, and (d) centralized administration by the RosettaCommons to ensure continuous maintenance. This paper describes the ROSIE server infrastructure, a step-by-step ‘serverification’ protocol for use by Rosetta developers, and the deployment of the first nine ROSIE applications by six separate developer teams: Docking, RNA de novo, ERRASER, Antibody, Sequence Tolerance, Supercharge, Beta peptide design, NCBB design, and VIP redesign. As illustrated by the number and diversity of these applications, ROSIE offers a general and speedy paradigm for serverification of Rosetta applications that incurs negligible cost to developers and lowers barriers to Rosetta use for the broader biological community. ROSIE is available at http://rosie.rosettacommons.org.
Highlights
The Rosetta molecular modeling suite provides tools for a wide range of fundamental questions in structural biology, from the engineering of novel protein enzymes to the prediction of large non-coding RNA structures
The current codebase is rapidly evolving due to the efforts of more than 250 active developers, ease of integrating new functionality into a modular software architecture [1], cross-fertilization between teams working on different systems, and continuing improvements inspired by stringent experimental tests and blind prediction contests [2]
We have developed a core web server infrastructure called Rosetta Online Server That Includes Everyone (ROSIE), the Rosetta Online Server that Includes Everyone, to lower barriers to Rosetta application deployment as servers
Summary
The Rosetta molecular modeling suite provides tools for a wide range of fundamental questions in structural biology, from the engineering of novel protein enzymes to the prediction of large non-coding RNA structures. Most of the 50+ applications in the Rosetta package require familiarity with a Unix environment, access to a high-performance computing cluster, and familiarity with tools to visualize and interpret results. Separate teams of Rosetta developers have created and added functionality to free web interfaces to nine protocols (Table 1) [9,10,11,12,13,14,15]. These servers are in high demand from the academic community, with wait times of at least a day in most cases. The vast majority of Rosetta applications are not available on servers
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