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Supported Applications

RFDesign

  • Description

    protein hallucination and inpainting with RoseTTAFold.

  • Usage Notes

    RFDesign in SBGrid/BioGrids provides the following callable executables:

    python.rfdesign

    hallucinate.py

    inpaint.py

    Use python.rfdesign when calling scripts:

    $ python.rfdesign hallucinate.py

    or call the scripts directly (without a path):

    $ hallucinate.py

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install rfdesign Copy to clipboard

  • Primary Citation*

    J. Wang, S. Lisanza, D. Juergens, D. Tischer, I. Anishchenko, M. Baek, J. L. Watson, J. H. Chun, L. F. Milles, J. Dauparas, M. Expòsit, W. Yang, A. Saragovi, S. Ovchinnikov, and D. Baker. 2021. Deep learning methods for designing proteins scaffolding functional sites. bioRxiv 2021.11.10.468128.

    M. Baek, F. DiMaio, I. Anishchenko, J. Dauparas, S. Ovchinnikov, G. R. Lee, J. Wang, Q. Cong, L. N. Kinch, R. D. Schaeffer, C. Millán, H. Park, C. Adams, C. R. Glassman, A. DeGiovanni, J. H. Pereira, A. V. Rodrigues, A. A. van Dijk, A. C. Ebrecht, D. J. Opperman, T. Sagmeister, C. Buhlheller, T. Pavkov-Keller, M. K. Rathinaswamy, U. Dalwadi, C. K. Yip, J. E. Burke, K. C. Garcia, N. V. Grishin, P. D. Adams, R. J. Read, and D. Baker. 2021. Accurate prediction of protein structures and interactions using a three-track neural network. Science. 373(6557): 871-876.


    • *Full citation information available through

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