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Information-Driven Modelling of Antibody-Antigen Complexes

39 Pages Posted: 1 Apr 2019 Sneak Peek Status: Published

See all articles by F. Ambrosetti

F. Ambrosetti

University of Rome I - Department of Physics; Utrecht University - Computational Structural Biology Group

B. Jiménez-García

Utrecht University - Computational Structural Biology Group

J. Roel-Touris

Utrecht University - Computational Structural Biology Group

A.M.J.J. Bonvin

Utrecht University - Computational Structural Biology Group

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Abstract

Antibodies are Y-shaped proteins essential for immune response. Their capability to recognize antigens with high specificity makes them excellent therapeutic targets. Understanding the structural basis of antibody-antigen interactions is therefore crucial to improve our ability of designing efficient biological drugs. Computational approaches such as molecular docking are providing a valuable and fast alternative to experimental structural characterization for those complexes. We investigate here how information about complementary determining regions and binding epitopes can be used to drive the modelling process and present a comparative study of four different docking software (ClusPro, LightDock, ZDOCK and HADDOCK) providing specific options for antibody-antigen modelling. Their performance on a dataset of 16 complexes is reported. HADDOCK, which includes information to drive the docking, is shown to perform best in terms of both success rate and quality of the generated models both in the presence and absence of information about the epitope on the antigen.

Keywords: Antibody, docking, H3-modelling, ClusPro, ZDOCK, HADDOCK, LightDock

Suggested Citation

Ambrosetti, F. and Jiménez-García, B. and Roel-Touris, J. and Bonvin, A.M.J.J., Information-Driven Modelling of Antibody-Antigen Complexes (March 29, 2019). Available at SSRN: https://ssrn.com/abstract=3362436 or http://dx.doi.org/10.2139/ssrn.3362436
This is a paper under consideration at Cell Press and has not been peer-reviewed.

F. Ambrosetti

University of Rome I - Department of Physics

Piazzale Aldo Moro, 5
Rome, 00185
Italy

Utrecht University - Computational Structural Biology Group

3584CH Utrecht
Netherlands

B. Jiménez-García

Utrecht University - Computational Structural Biology Group

3584CH Utrecht
Netherlands

J. Roel-Touris

Utrecht University - Computational Structural Biology Group

3584CH Utrecht
Netherlands

A.M.J.J. Bonvin (Contact Author)

Utrecht University - Computational Structural Biology Group ( email )

3584CH Utrecht
Netherlands

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