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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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.
The authors declare no competing financial interests.
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Weitzner, B., Jeliazkov, J., Lyskov, S. et al. Modeling and docking of antibody structures with Rosetta. Nat Protoc 12, 401–416 (2017). https://doi.org/10.1038/nprot.2016.180
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