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Abstract

We describe Rosetta-based computational protocols for predicting the 3D structure of an antibody from sequence (RosettaAntibody) and then docking the antibody to protein antigens (SnugDock). Antibody modeling leverages canonical loop conformations to graft large segments from experimentally determined structures, as well as offering (i) energetic calculations to minimize loops, (ii) docking methodology to refine the VL–VH relative orientation and (iii) de novo prediction of the elusive complementarity determining region (CDR) H3 loop. To alleviate model uncertainty, antibody–antigen docking resamples CDR loop conformations and can use multiple models to represent an ensemble of conformations for the antibody, the antigen or both. These protocols can be run fully automated via the ROSIE web server (http://rosie.rosettacommons.org/) or manually on a computer with user control of individual steps. For best results, the protocol requires roughly 1,000 CPU-hours for antibody modeling and 250 CPU-hours for antibody–antigen docking. Tasks can be completed in under a day by using public supercomputers.

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Change history

  • 14 December 2017

    In the version of this article initially published, Box 4 was omitted. The corrected article now includes Box 4. This error has been corrected in the HTML and PDF versions of the article.

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Acknowledgements

The authors thank A. Sivasubramanian, A. Sircar and S. Chaudhury for their development of the original RosettaAntibody, SnugDock and EnsembleDock methods. J. Xu refactored the antibody code. We also thank the members of the RosettaCommons for the continued development of the Rosetta Software Suite. ROSIE simulations were carried out, in part, within the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant no. ACI-1053575. B.D.W., N.M., J.R.J., R.L.D. and J.J.G. are supported by National Institutes of Health grant no. R01 GM078221. S.L. is supported by National Institutes of Health grant no. R01 GM73151. D.K. is supported by the DARPA Antibody Technology Program (grant no. HR-0011-10-1-0052) and the Japan Society for the Promotion of Science (grant no. 15H06606). R.F. is supported by the South-Eastern Norway Regional Health Authority (grant no. 850703-6051-39788). J.A.-B. and R.L.D. are supported by National Institutes of Health grant nos. R01 GM111819 and R01 GM084453.

Author information

Author notes

    • Brian D Weitzner
    • , Jeliazko R Jeliazkov
    •  & Sergey Lyskov

    These authors contributed equally to this work.

Affiliations

  1. Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA.

    • Brian D Weitzner
    • , Sergey Lyskov
    • , Nicholas Marze
    • , Daisuke Kuroda
    • , Naireeta Biswas
    •  & Jeffrey J Gray
  2. Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, USA.

    • Jeliazko R Jeliazkov
    •  & Jeffrey J Gray
  3. Department of Analytical and Physical Chemistry, Showa University School of Pharmacy, Tokyo, Japan.

    • Daisuke Kuroda
  4. Centre for Immune Regulation, Department of Biosciences, University of Oslo, Oslo, Norway.

    • Rahel Frick
  5. Centre for Immune Regulation, Department of Immunology, Oslo University Hospital Rikshospitalet, Oslo, Norway.

    • Rahel Frick
  6. Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA.

    • Jared Adolf-Bryfogle
  7. Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA.

    • Jared Adolf-Bryfogle
    •  & Roland L Dunbrack Jr
  8. Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, USA.

    • Jeffrey J Gray
  9. Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA.

    • Jeffrey J Gray

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Contributions

B.D.W., N.M., S.L., D.K., J.R.J., J.A.-B., R.L.D. and J.J.G. developed the current version of RosettaAntibody. S.L. developed ROSIE and implemented the RosettaAntibody and SnugDock server applications. B.D.W. implemented SnugDock in Rosetta 3, and J.R.J. benchmarked SnugDock's performance. R.F. and N.B. wrote the procedure, codified the manual intervention steps developed by B.D.W., N.M. and D.K., and recorded timing information. B.D.W., J.R.J., N.M., S.L., D.K., R.F., J.A.-B., N.B., R.L.D. and J.J.G. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Jeffrey J Gray.

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    Supplementary Tutorial

    Worked example of humanized Fab D3h44 in complex with tissue factor.

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DOI

https://doi.org/10.1038/nprot.2016.180

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