Modeling and docking of antibody structures with Rosetta.

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 V_L-V_H 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 autom

SUBMITTER: Weitzner BD 

PROVIDER: S-EPMC5739521 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature