Modeling and docking antibody structures with Rosetta
Brian D. Weitzner,
Jeliazko R. Jeliazkov,
Jeffrey J. Gray
Posted 16 Aug 2016
bioRxiv DOI: 10.1101/069930 (published DOI: 10.1038/nprot.2016.180)
Posted 16 Aug 2016
We describe Rosetta-based computational protocols for predicting the three-dimensional structure of an antibody from sequence and then docking the antibody--protein-antigen complexes. Antibody modeling leverages canonical loop conformations to graft large segments from experimentally-determined structures as well as (1) energetic calculations to minimize loops, (2) docking methodology to refine the VL--VH relative orientation, and (3) 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 or manually on a computer with user control of individual steps. For best results, the protocol requires roughly 2,500 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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