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Rosetta++
License:
Rosetta++ Software
Academic License Agreement
The University of Washington (“UW”) and the developers of the Rosetta software (Developers) give permission for you (“You”) and your Institution (“Institution”) to use the Rosetta++ protein prediction software (“Software”). Software was developed through support from the National Institutes of Health, Human Frontier Science Program Grant, National Science Foundation, Office of Naval Research, Packard Foundation, the Damon Runyon Cancer Research Foundation, Jane Coffin Childs Foundation, Los Alamos National Lab, and in part by researchers of the Howard Hughes Medical Institute (HHMI) at UW. UW and the Developers allow researchers at your Institution to copy and modify Software, for internal, non-profit research purposes, on the following conditions:
1. The Software remains at your Institution and is not published, distributed, or otherwise transferred or made available to other than Institution employees and students involved in research under your supervision.
2. You agree to make protein sequences, models and structures generated by using Software available to other academic researchers for non-profit research purposes. If You wish to obtain Software for any commercial purposes, including fee-based service projects, You will need to execute a separate licensing agreement with the University of Washington and pay a fee. In that case please contact: license@u.washington.edu
3. You retain in Software and any modifications to Software, the copyright, trademark, or other notices pertaining to Software as provided by UW.
4. You provide the Developers with feedback on the use of the Software in your research, and that the Developers and UW are permitted to use any information You provide in making changes to the Software. All bug reports and technical questions shall be sent to the email address: general-support@rosettacommons.org
5. You acknowledge that the Developers, HHMI, UW and its licensees may develop modifications to Software that may be substantially similar to your modifications of Software, and that the Developers, HHMI, UW and its licensees shall not be constrained in any way by You in HHMI’s, UW’s or its licensees’ use or management of such modifications. You acknowledge the right of the Developers, HHMI, and UW to prepare and publish modifications to Software that may be substantially similar or functionally equivalent to your modifications and improvements, and if You obtain patent protection for any modification or improvement to Software You agree not to allege or enjoin infringement of your patent by the Developers, HHMI, the UW or by any of UW’s licensees obtaining modifications or improvements to Software from the University of Washington or the Developers.
6. We will acknowledge in our publications contributions we make to each other’s research involving or based on the Software. The current citations for Software are:
Rosetta ab initio structure prediction
Bonneau R, Strauss CE, Rohl CA, Chivian D, Bradley P, Malmstrom L, Robertson T, Baker D. (2002) De novo prediction of three-dimensional structures for major protein families. J Mol Biol 322(1):65-78.
Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CE, Baker D. (2001) Rosetta in CASP4: progress in ab initio protein structure prediction. Proteins Suppl 5:119-26.
Simons KT, Ruczinski I, Kooperberg C, Fox B, Bystroff C, Baker D. (1999) Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 34(1) 82-95.
Simons KT, Kooperberg C, Huang E, Baker, D. (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulate anealing and Bayesian scoring functions. J Mol Biol 268:209-25.
RosettaDock
Protein-Protein Docking with Simultaneous Optimization of Rigid Body Displacement and Side Chain Conformations, J.J. Gray, S.E. Moughan, C. Wang, O. Schueler-Furman, B. Kuhlman, C.A. Rohl and D. Baker, J. Mol. Biol., 331(1), 281-299, 2003.
Protein-Protein Docking Predictions for the CAPRI Experiment, J.J. Gray, S.E. Moughan, T. Kortemme, O. Schueler-Furman, K.M.S. Misura, A.V. Morozov, and D. Baker, Proteins, 52(1), 118-122, 2003.
RosettaDesign
Dantas, G., Kuhlman, B., Callender, D., Wong, M., D. Baker: A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J Mol Biol 332: (2) 449-60 Sep 12 2003.
Kuhlman B, Dantas G, Ireton G, Varani G, Stoddard B, Baker D: Design of a novel globular protein fold with atomic level accuracy. Science, 302, 1364-1368, Nov 21 2003.
RosettaNMR
Rohl CA and Baker D. (2002) De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. J Am Chem Soc 124:2723-9.
Bowers PM, Strauss CE, Baker D. (2000) De novo protein structure determination using sparse NMR data. J Biomol NMR 18(4):311-8.
RosettaNucleicAcids
Havranek, J. J., Duarte, C. M., Baker, D. (2004). A simple physical model for the prediction and design of protein-DNA interactions J Mol Biol 344, 59-70.
RosettaLigand
Meiler J, Baker D. (2006). ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 65(3):538-48.
7. Any risk associated with using the Software at your institution is with You and your Institution. Software is experimental in nature and is made available as a research courtesy "AS IS," without obligation by UW to provide accompanying services or support.
8. UW AND THE AUTHORS EXPRESSLY DISCLAIM ANY AND ALL WARRANTIES REGARDING THE SOFTWARE, WHETHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES PERTAINING TO NON-INFRINGEMENT, MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.
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