@article {Weitzner069930, author = {Brian D. Weitzner and Jeliazko R. Jeliazkov and Sergey Lyskov and Nicholas Marze and Daisuke Kuroda and Rahel Frick and Naireeta Biswas and Jeffrey J. Gray}, title = {Modeling and docking antibody structures with Rosetta}, elocation-id = {069930}, year = {2016}, doi = {10.1101/069930}, publisher = {Cold Spring Harbor Laboratory}, abstract = {We describe Rosetta-based computational protocols for predicting the three-dimensional structure of an antibody from sequence and then docking the antibody{\textendash}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{\textendash}VH relative orientation, and (3) de novo prediction of the elusive complementarity determining region (CDR) H3 loop. To alleviate model uncertainty, antibody{\textendash}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{\textendash}antigen docking. Tasks can be completed in under a day by using public supercomputers.}, URL = {https://www.biorxiv.org/content/early/2016/08/16/069930}, eprint = {https://www.biorxiv.org/content/early/2016/08/16/069930.full.pdf}, journal = {bioRxiv} }