Rosetta is molecular modeling software that has been developed for the prediction and design of macromolecular structure. Rosetta has performed well in community wide assessments of protein structure prediction and docking, and it has been used to engineer proteins for a variety of applications including: scaffold design for vaccine development, biosensor design for live cell imaging, and protein interface design to create inhibitors of human pathogens. Rosetta is developed and maintained by research groups at over 20 universities, and over the 9 years since its first release, 9750 academic laboratories have obtained free licenses to use the software. This proposal is a competing renewal and is in response to a program announcement (PAR-11-028) for the continued development and maintenance of software. Activities from the previous funding periods have been instrumental in the productive growth of Rosetta, these include the creation of a C++ object-oriented version of Rosetta (from Fortran) that allows scientists to more easily combine alternate sampling protocols and energy functions, the development of an automated testing system for checking the integrity of the code base, deployment of web servers for more standard Rosetta simulations, and user support through an online forum system. With this proposal our goal is to further increase the usefulness of Rosetta to expert and non-expert users as well as promote the rapid development of new algorithms by maintaining a robust code base and a rigorous set of technical and scientific benchmarks.
Our specific aims i nclude the further development and extension of scripting tools for generating custom protocols, increasing the speed of Rosetta simulations through parallel computing, deployment of new automated tests to validate code accuracy and enforce coding standards, and user support through a unified web server for Rosetta applications.
The function of a protein, RNA or DNA molecule is largely determined by its 3-dimensional structure. We aim to develop a state-of-the-art computer program for predicting and designing the structures of biological macromolecules. The program will be freely available to academic laboratories and its predictions will help investigators understand and fight human diseases such as cancer and AIDS.
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