Rosetta – The premier software suite for macromolecular modeling

Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids. Since 1998, Rosetta web servers have run billions of structure prediction and protein design simulations.

Researchers use Rosetta to better understand treatments of infectious diseases, cancers, and autoimmune disorders. Further applications involve the development of vaccines, new materials, targeted protein binders, and enzyme design.

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Rosetta began as a structure prediction tool, and has consistently been a strong performer in Critical Assessment of Structure Prediction (CASP) competitions. It has grown to offer a wide variety of effective sampling algorithms to explore backbone, side-chain and sequence space. Rosetta boasts broadly tested scoring (energy) functions and contains an unparalleled breadth of applications from folding to docking to design.

Rosetta is freely available to academic and government laboratories, with over 10,000 free licenses already in use. An active support forum allows users to easily collaborate within the broad research community of Rosetta users.

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Related research includes:

Structures of designed enzymes. Jiang L, et al (2008). De novo computational design of retro-aldol enzymes.Science 319, 1387-91.

1.6 Å C{alpha}-RMSD blind structure prediction for CASP6 target T0281, hypothetical protein from Thermus thermophilus Hb8.(Bradley P, Misura KM, Baker D, (2005) Science. 309:1868-71.)
Ribbon diagrams of Top7 with residues 46 to 76 highlighted in red -- A novel protein structure created with RosettaDesign.(Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D, Science 302, 1364-8.)

Welcome to RosettaCommons

RosettaCommons is the central hub for over 150 developers from 23 universities and laboratories to contribute and share the Rosetta source code. The RosettaCommons hosts a source code repository, this informational website, a support forum, and annual conferences to facilitate communication between developers.

RosettaCommons: An Innovative Collaboration

RosettaCommons has a unique agreement among member universities. The source code belongs to the RosettaCommons members and is a collaborative effort among research institutions, a model that promotes shared development and discoveries. RosettaCommons makes close collaboration between laboratories the norm, even with single code modules.

The Rosetta Impact

Rosetta is not restricted to academic laboratories. Government laboratories, institutes, research centers, and partner corporations also use Rosetta software. Rosetta has been featured in over 700 publications, which in turn have been cited over 25,000 times. Early successes in protein design breakthroughs include determining the first crystal structure of a TAL protein, the design of inhibitors of amyloid fibril formation, and the modeling of protein complexes in the ubiquitination pathway.

Related Projects

  • Foldit – A fun, visual game for any person, scientist or non-scientist, to solve protein folding problems. Your handmade protein folding solutions help us improve our computation algorithms!
  • Rosetta@home – Run Rosetta@home on your home computer and contribute your unused processor time to help scientists speed up their protein structure calculations.
  • ROSIE: Rosetta Server that Includes Everyone hosts several servers for combined computer power as a free resource for academic users.

Rosetta Scripting Tools

  • PyRosetta - A set of Python bindings that provides the ability to access, modify, and extend Rosetta C++ objects using the Python programming language. PyRosetta is ideal for creating new protocols by combining existing routines or writing new “Movers” and score terms. PyRosetta is excellent for teaching introductory material to the field.
  • RosettaScripts - An XML script interface that allows users to mix and match those Rosetta protocols that have been exposed to the RosettaScript framework. Unlike PyRosetta, RosettaScripts does not yet have direct access to all of Rosetta’s C++ objects, but it does have the advantage that it is part of the standard C++ build of Rosetta, whereas PyRosetta requires a separate build process that is sensitive to the operating system and associated libraries. Therefore, it is straightforward to use RosettaScripts on large supercomputers and distributed computing environments such as BOINC.

Previous Grant Accomplishments (2009-2013)

In the last four years, RosettaCommons has implemented many improvements:

  1. Completed the refactoring of Rosetta using object-oriented programming to create a set of modular libraries for energy calculation, conformational sampling, and sequence optimization that can be combined through common interfaces.
  2. Sped up Rosetta by taking advantage of the new C++ objects for caching energies and coordinates.
  3. Developed visualization tools for interacting with Rosetta simulations, and
  4. Enabled community wide Rosetta development and use.

The Next Steps for Rosetta and the RosettaCommons (2013 and beyond)

  1. Expanding two scripting interfaces for generating custom protocols
  2. Increasing the speed of Rosetta calculations
  3. Developing the automatic testing system with static analysis tools
  4. Providing a unified web server and additional user support