posted on 2021-03-11, 17:34authored byClara
T. Schoeder, Samuel Schmitz, Jared Adolf-Bryfogle, Alexander M. Sevy, Jessica A. Finn, Marion F. Sauer, Nina G. Bozhanova, Benjamin K. Mueller, Amandeep K. Sangha, Jaume Bonet, Jonathan H. Sheehan, Georg Kuenze, Brennica Marlow, Shannon T. Smith, Hope Woods, Brian J. Bender, Cristina E. Martina, Diego del Alamo, Pranav Kodali, Alican Gulsevin, William R. Schief, Bruno E. Correia, James E. Crowe, Jens Meiler, Rocco Moretti
Structure-based antibody
and antigen design has advanced greatly
in recent years, due not only to the increasing availability of experimentally
determined structures but also to improved computational methods for
both prediction and design. Constant improvements in performance within
the Rosetta software suite for biomolecular modeling have given rise
to a greater breadth of structure prediction, including docking and
design application cases for antibody and antigen modeling. Here,
we present an overview of current protocols for antibody and antigen
modeling using Rosetta and exemplify those by detailed tutorials originally
developed for a Rosetta workshop at Vanderbilt University. These tutorials
cover antibody structure prediction, docking, and design and antigen
design strategies, including the addition of glycans in Rosetta. We
expect that these materials will allow novice users to apply Rosetta
in their own projects for modeling antibodies and antigens.