Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

Clara 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

doi:10.1021/acs.biochem.0c00912

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

Clara 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 GulsevinWilliam R. Schief, Bruno E. Correia, James E. Crowe, Jens Meiler, Rocco Moretti

Division of Infectious Diseases

Research output: Contribution to journal › Article › peer-review

35 Scopus citations

Abstract

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.

Original language	English
Pages (from-to)	825-846
Number of pages	22
Journal	Biochemistry
Volume	60
Issue number	11
DOIs	https://doi.org/10.1021/acs.biochem.0c00912
State	Published - Mar 23 2021

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Schoeder, C. T., Schmitz, S., Adolf-Bryfogle, J., Sevy, A. M., Finn, J. A., Sauer, M. F., Bozhanova, N. G., Mueller, B. K., Sangha, A. K., Bonet, J., Sheehan, J. H., Kuenze, G., Marlow, B., Smith, S. T., Woods, H., Bender, B. J., Martina, C. E., Del Alamo, D., Kodali, P., ... Moretti, R. (2021). Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design. Biochemistry, 60(11), 825-846. https://doi.org/10.1021/acs.biochem.0c00912

@article{4203714dde4241b885eb90e2e6eda870,

title = "Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design",

abstract = "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.",

author = "Schoeder, {Clara T.} and Samuel Schmitz and Jared Adolf-Bryfogle and Sevy, {Alexander M.} and Finn, {Jessica A.} and Sauer, {Marion F.} and Bozhanova, {Nina G.} and Mueller, {Benjamin K.} and Sangha, {Amandeep K.} and Jaume Bonet and Sheehan, {Jonathan H.} and Georg Kuenze and Brennica Marlow and Smith, {Shannon T.} and Hope Woods and Bender, {Brian J.} and Martina, {Cristina E.} and {Del Alamo}, Diego and Pranav Kodali and Alican Gulsevin and Schief, {William R.} and Correia, {Bruno E.} and Crowe, {James E.} and Jens Meiler and Rocco Moretti",

note = "Publisher Copyright: {\textcopyright} 2021 The Authors. Published by American Chemical Society.",

year = "2021",

month = mar,

day = "23",

doi = "10.1021/acs.biochem.0c00912",

language = "English",

volume = "60",

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Schoeder, CT, Schmitz, S, Adolf-Bryfogle, J, Sevy, AM, Finn, JA, Sauer, MF, Bozhanova, NG, Mueller, BK, Sangha, AK, Bonet, J, Sheehan, JH, Kuenze, G, Marlow, B, Smith, ST, Woods, H, Bender, BJ, Martina, CE, Del Alamo, D, Kodali, P, Gulsevin, A, Schief, WR, Correia, BE, Crowe, JE, Meiler, J & Moretti, R 2021, 'Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design', Biochemistry, vol. 60, no. 11, pp. 825-846. https://doi.org/10.1021/acs.biochem.0c00912

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T1 - Modeling Immunity with Rosetta

T2 - Methods for Antibody and Antigen Design

AU - Schoeder, Clara T.

AU - Schmitz, Samuel

AU - Adolf-Bryfogle, Jared

AU - Sevy, Alexander M.

AU - Finn, Jessica A.

AU - Sauer, Marion F.

AU - Bozhanova, Nina G.

AU - Mueller, Benjamin K.

AU - Sangha, Amandeep K.

AU - Bonet, Jaume

AU - Sheehan, Jonathan H.

AU - Kuenze, Georg

AU - Marlow, Brennica

AU - Smith, Shannon T.

AU - Woods, Hope

AU - Bender, Brian J.

AU - Martina, Cristina E.

AU - Del Alamo, Diego

AU - Kodali, Pranav

AU - Gulsevin, Alican

AU - Schief, William R.

AU - Correia, Bruno E.

AU - Crowe, James E.

AU - Meiler, Jens

AU - Moretti, Rocco

PY - 2021/3/23

Y1 - 2021/3/23

N2 - 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.

AB - 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.

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SN - 0006-2960

VL - 60

SP - 825

EP - 846

JO - Biochemistry

JF - Biochemistry

IS - 11

ER -

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

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