The HADDOCK2.4 web server for integrative modeling of biomolecular complexes

Rodrigo V Vargas Honorato; Mikael E Trellet; Brian Jiménez-García; Jörg J Schaarschmidt; Marco Giulini; Victor Reys; Panagiotis I Koukos; João P G L M Rodrigues; Ezgi Karaca; Gydo C P van Zundert; Jorge Roel-Touris; Charlotte W van Noort; Zuzana Jandová; Adrien S J Melquiond; Alexandre M J J Bonvin

doi:10.1038/s41596-024-01011-0

The HADDOCK2.4 web server for integrative modeling of biomolecular complexes

Rodrigo V Vargas Honorato, Mikael E Trellet, Brian Jiménez-García, Jörg J Schaarschmidt, Marco Giulini, Victor Reys, Panagiotis I Koukos, João P G L M Rodrigues, Ezgi Karaca, Gydo C P van Zundert, Jorge Roel-Touris, Charlotte W van Noort, Zuzana Jandová, Adrien S J Melquiond, Alexandre M J J Bonvin^*

^*Corresponding author for this work

Utrecht University

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

Abstract

Interactions between macromolecules, such as proteins and nucleic acids, are essential for cellular functions. Experimental methods can fail to provide all the information required to fully model biomolecular complexes at atomic resolution, particularly for large and heterogeneous assemblies. Integrative computational approaches have, therefore, gained popularity, complementing traditional experimental methods in structural biology. Here, we introduce HADDOCK2.4, an integrative modeling platform, and its updated web interface ( https://wenmr.science.uu.nl/haddock2.4 ). The platform seamlessly integrates diverse experimental and theoretical data to generate high-quality models of macromolecular complexes. The user-friendly web server offers automated parameter settings, access to distributed computing resources, and pre- and post-processing steps that enhance the user experience. To present the web server's various interfaces and features, we demonstrate two different applications: (i) we predict the structure of an antibody-antigen complex by using NMR data for the antigen and knowledge of the hypervariable loops for the antibody, and (ii) we perform coarse-grained modeling of PRC1 with a nucleosome particle guided by mutagenesis and functional data. The described protocols require some basic familiarity with molecular modeling and the Linux command shell. This new version of our widely used HADDOCK web server allows structural biologists and non-experts to explore intricate macromolecular assemblies encompassing various molecule types.

Original language	English
Pages (from-to)	3219-3241
Number of pages	23
Journal	Nature protocols
Volume	19
Issue number	11
Early online date	17 Jun 2024
DOIs	https://doi.org/10.1038/s41596-024-01011-0
Publication status	Published - Nov 2024

Bibliographical note

Publisher Copyright:
© Springer Nature Limited 2024.

Funding

The authors acknowledge financial support from the European Union Horizon 2020, projects BioExcel (675728, 823830), from the EuroHPC Joint Undertaking and Sweden, Netherlands, Germany, Spain, Finland and Norway (101093290) and from the Dutch Foundation for Scientific Research (NWO) (TOP-PUNT grant 718.015.001). The FP7 WeNMR (261572), H2020 West-Life (675858), EOSC-hub (777536) and EGI-ACE (101017567) European e-Infrastructure projects are acknowledged for the use of the EGI infrastructure with the dedicated support of CESNET-MCC, INFN-LNL-2, NCG-INGRID-PT, TW-NCHC, CESGA, IFCA-LCG2, UA-BITP, TR-FC1-ULAKBIM, CSTCLOUD-EGI, IN2P3-CPPM, CIRMMP, SURFsara and NIKHEF and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, Taiwan and the US Open Science Grid.

Funders	Funder number
Dutch Foundation for Scientific Research
Horizon 2020	823830, 675728
European High Performance Computing Joint Undertaking	101093290
Nederlandse Organisatie voor Wetenschappelijk Onderzoek	718.015.001

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10.1038/s41596-024-01011-0

s41596-024-01011-0Final published version, 6.01 MBLicence: Taverne

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Vargas Honorato, R. V., Trellet, M. E., Jiménez-García, B., Schaarschmidt, J. J., Giulini, M., Reys, V., Koukos, P. I., Rodrigues, J. P. G. L. M., Karaca, E., van Zundert, G. C. P., Roel-Touris, J., van Noort, C. W., Jandová, Z., Melquiond, A. S. J., & Bonvin, A. M. J. J. (2024). The HADDOCK2.4 web server for integrative modeling of biomolecular complexes. Nature protocols, 19(11), 3219-3241. https://doi.org/10.1038/s41596-024-01011-0

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abstract = "Interactions between macromolecules, such as proteins and nucleic acids, are essential for cellular functions. Experimental methods can fail to provide all the information required to fully model biomolecular complexes at atomic resolution, particularly for large and heterogeneous assemblies. Integrative computational approaches have, therefore, gained popularity, complementing traditional experimental methods in structural biology. Here, we introduce HADDOCK2.4, an integrative modeling platform, and its updated web interface ( https://wenmr.science.uu.nl/haddock2.4 ). The platform seamlessly integrates diverse experimental and theoretical data to generate high-quality models of macromolecular complexes. The user-friendly web server offers automated parameter settings, access to distributed computing resources, and pre- and post-processing steps that enhance the user experience. To present the web server's various interfaces and features, we demonstrate two different applications: (i) we predict the structure of an antibody-antigen complex by using NMR data for the antigen and knowledge of the hypervariable loops for the antibody, and (ii) we perform coarse-grained modeling of PRC1 with a nucleosome particle guided by mutagenesis and functional data. The described protocols require some basic familiarity with molecular modeling and the Linux command shell. This new version of our widely used HADDOCK web server allows structural biologists and non-experts to explore intricate macromolecular assemblies encompassing various molecule types.",

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Vargas Honorato, RV, Trellet, ME, Jiménez-García, B, Schaarschmidt, JJ, Giulini, M , Reys, V, Koukos, PI, Rodrigues, JPGLM, Karaca, E, van Zundert, GCP, Roel-Touris, J, van Noort, CW, Jandová, Z, Melquiond, ASJ & Bonvin, AMJJ 2024, 'The HADDOCK2.4 web server for integrative modeling of biomolecular complexes', Nature protocols, vol. 19, no. 11, pp. 3219-3241. https://doi.org/10.1038/s41596-024-01011-0

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AU - Schaarschmidt, Jörg J

AU - Giulini, Marco

AU - Reys, Victor

AU - Koukos, Panagiotis I

AU - Rodrigues, João P G L M

AU - Karaca, Ezgi

AU - van Zundert, Gydo C P

AU - Roel-Touris, Jorge

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The HADDOCK2.4 web server for integrative modeling of biomolecular complexes

Abstract

Bibliographical note

Funding

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