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The HADDOCK2.4 web server for integrative modeling of biomolecular complexes
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Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
MolProbity : all-atom structure validation for macromolecular crystallography
Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909042073 · Cited by 14,115
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Varadi, M., Anyango, S., Deshpande, M., Nair, S., Natassia, C., Yordanova, G., Yuan, D., Stroe, O., Wood, G., Laydon, A., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1061 · Cited by 7,850
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Accurate prediction of protein structures and interactions using a 3-track network
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HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
Dominguez, C., Boelens, R., & Bonvin, A. M. J. J. (2003) · Journal of the American Chemical Society · doi:10.1021/ja026939x · Cited by 3,187
Self-citationOpenMM 7: Rapid development of high performance algorithms for molecular dynamics
Eastman, P., Swails, J., Chodera, J. D., McGibbon, R. T., Zhao, Y., Beauchamp, K. A., Wang, L.-P., Simmonett, A. C., Harrigan, M. P., Stern, C. D., et al. (2017) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1005659 · Cited by 2,748
Harnessing protein folding neural networks for peptide–protein docking
Tsaban, T., Varga, J. K., Avraham, O., Ben-Aharon, Z., Khramushin, A., & Schueler-Furman, O. (2022) · Nature Communications · doi:10.1038/s41467-021-27838-9 · Cited by 1,205
Research works printed but not linked: 43
- van Noort, C. W., Honorato, R. V. & Bonvin, A. M. J. J. Information-driven modeling of biomolecular complexes. Curr. Opin. Struct. Biol. 70, 70–77 (2021). · DOI
- Masrati, G. et al. Integrative structural biology in the era of accurate structure prediction. J. Mol. Biol. 433, 167127 (2021). · DOI · Paper page
- Rout, M. P. & Sali, A. Principles for integrative structural biology studies. Cell 177, 1384–1403 (2019). · DOI · Paper page
- Perrakis, A. & Sixma, T. K. AI revolutions in biology. EMBO Rep. 22, e54046 (2021). · DOI · Paper page
- Vakser, I. A. & Deeds, E. J. Computational approaches to macromolecular interactions in the cell. Curr. Opin. Struct. Biol. 55, 59–65 (2019). · DOI
- wwPDB Consortium. Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucleic Acids Res. 47, D520–D528 (2018). · DOI · Paper page
- Sali, A. et al. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure 23, 1156–1167 (2015). · DOI
- Vallat, B. et al. New system for archiving integrative structures. Acta Crystallogr. D. Struct. Biol. 77, 1486–1496 (2021). · DOI
- Saponaro, A., Maione, V., Bonvin, A. & Cantini, F. Understanding docking complexes of macromolecules using HADDOCK: the synergy between experimental data and computations. Bio-Protoc. 10, e3793 (2020). · DOI
- Roel-Touris, J., Jiménez-García, B. & Bonvin, A. M. J. J. Integrative modeling of membrane-associated protein assemblies. Nat. Commun. 11, 6210 (2020). · DOI
- Ambrosetti, F., Jandova, Z. & Bonvin, A. M. J. J. Information-driven antibody–antigen modelling with HADDOCK. In: Methods in Molecular Biology Vol. 2552 (eds Tsumoto, K. & Kuroda, D.) 267–282 (Humana, 2023). · DOI
- Ambrosetti, F., Jiménez-García, B., Roel-Touris, J. & Bonvin, A. M. J. J. Modeling antibody-antigen complexes by information-driven docking. Structure 28, 119–129.e2 (2020). · DOI
- Trellet, M., van Zundert, G. & Bonvin, A. M. J. J. Structural bioinformatics, methods and protocols. Methods Mol. Biol. 2112, 145–162 (2020). · doi:10.1007/978-1-0716-0270-6_11
- Koukos, P. I. & Bonvin, A. M. J. J. Integrative modelling of biomolecular complexes. J. Mol. Biol. 432, 2861–2881 (2020). · DOI
- Rosell, M. & Fernández-Recio, J. Docking approaches for modeling multi-molecular assemblies. Curr. Opin. Struct. Biol. 64, 59–65 (2020). · DOI
- Roel-Touris, J., Bonvin, A. M. J. J. & Jiménez-García, B. LightDock goes information-driven. Bioinformatics 36, 950–952 (2019). · DOI
- Xia, B., Vajda, S. & Kozakov, D. Accounting for pairwise distance restraints in FFT-based protein–protein docking. Bioinformatics 32, 3342–3344 (2016). · DOI
- Echartea, M. E. R., Ritchie, D. W. & de Beauchêne, I. C. Using restraints in EROS‐DOCK improves model quality in pairwise and multicomponent protein docking. Proteins 88, 1121–1128 (2020). · DOI
- Bryant, P. et al. Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search. Nat. Commun. 13, 6028 (2022). · doi:10.1038/s41467-022-33729-4
- Brünger, A. T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D. Biol. Crystallogr. 54, 905–921 (1998). · DOI · Paper page
- de Vries, S. J., van Dijk, M. & Bonvin, A. M. J. J. The HADDOCK web server for data-driven biomolecular docking. Nat. Protoc. 5, 883–897 (2010). · DOI · Paper page
- van Zundert, G. C. P. et al. The HADDOCK2.2 web server: user-friendly integrative modeling of biomolecular complexes. J. Mol. Biol. 428, 720–725 (2016). · DOI · Paper page
- Roel-Touris, J., Don, C. G., Honorato, R. V., Rodrigues, J. P. G. L. M. & Bonvin, A. M. J. J. Less is more: coarse-grained integrative modeling of large biomolecular assemblies with HADDOCK. J. Chem. Theory Comput. 15, 6358–6367 (2019). · DOI
- Honorato, R. V., Roel-Touris, J. & Bonvin, A. M. J. J. MARTINI-based protein-DNA coarse-grained HADDOCKing. Front. Mol. Biosci. 6, 102 (2019). · DOI
- Marrink, S. J., Risselada, H. J., Yefimov, S., Tieleman, D. P. & de Vries, A. H. The MARTINI force field: coarse grained model for biomolecular simulations. J. Phys. Chem. B 111, 7812–7824 (2007). · DOI · Paper page
- van Zundert, G. C. P. & Bonvin, A. M. J. J. Defining the limits and reliability of rigid-body fitting in cryo-EM maps using multi-scale image pyramids. J. Struct. Biol. 195, 252–258 (2016). · doi:10.1016/j.jsb.2016.06.011
- Neijenhuis, T., Keulen, S. Cvan & Bonvin, A. M. J. J. Interface refinement of low- to medium-resolution cryo-EM complexes using HADDOCK2.4. Structure 30, 476–484 (2021). · DOI
- Koukos, P. I., Réau, M. & Bonvin, A. M. J. J. Shape-restrained modeling of protein–small-molecule complexes with high ambiguity driven DOCKing. J. Chem. Inf. Model 61, 4807–4818 (2021). · DOI
- Honorato, R. V. et al. Structural biology in the clouds: the WeNMR-EOSC ecosystem. Front. Mol. Biosci. 8, 729513 (2021). · DOI · Paper page
- Schüttelkopf, A. W. & van Aalten, D. M. F. PRODRG: a tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallogr. D. Biol. l Crystallogr. 60, 1355–1363 (2004). · DOI · Paper page
- Jorgensen, W. L. & Tirado-Rives, J. The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110, 1657–1666 (1988). · DOI · Paper page
- Fernández-Recio, J., Totrov, M. & Abagyan, R. Identification of protein–protein interaction sites from docking energy landscapes. J. Mol. Biol. 335, 843–865 (2004). · DOI · Paper page
- Veerapandian, B. et al. Functional implications of interleukin‐1β based on the three‐dimensional structure. Proteins 12, 10–23 (1992). · DOI
- Blech, M. et al. One target—two different binding modes: structural insights into gevokizumab and canakinumab interactions to interleukin-1β. J. Mol. Biol. 425, 94–111 (2013). · DOI
- Rodrigues, J. P. G. L. M., Teixeira, J. M. C., Trellet, M. & Bonvin, A. M. J. J. pdb-tools: a swiss army knife for molecular structures. F1000Res. 7, 1961 (2018). · DOI
- Mattiroli, F., Uckelmann, M., Sahtoe, D. D., van Dijk, W. J. & Sixma, T. K. The nucleosome acidic patch plays a critical role in RNF168-dependent ubiquitination of histone H2A. Nat. Commun. 5, 3291 (2014). · DOI
- McGinty, R. K., Henrici, R. C. & Tan, S. Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome. Nature 514, 591–596 (2014). · DOI · Paper page
- Bentley, M. L. et al. Recognition of UbcH5c and the nucleosome by the Bmi1/Ring1b ubiquitin ligase complex. EMBO J. 30, 3285–3297 (2011). · DOI
- Blech, M. & Hoerer, S. Crystal structure of human IL-1beta in complex with therapeutic antibody binding fragment of gevokizumab. Available at https://www.rcsb.org/structure/4g6m (2012). · doi:10.2210/pdb4g6m/pdb
- Tjandra, N., Omichinski, J. G., Gronenborn, A. M., Clore, G. M. & Bax, A. Use of dipolar 1H–15N and 1H–13C couplings in the structure determination of magnetically oriented macromolecules in solution. Nat. Struct. Biol. 4, 732–738 (1997). · DOI · Paper page
- Meiler, J., Blomberg, N., Nilges, M. & Griesinger, C. A new approach for applying residual dipolar couplings as restraints in structure elucidation. J. Biomol. NMR 16, 245–252 (2000). · doi:10.1023/a:1008378624590
- Banci, L. et al. Paramagnetism-based restraints for Xplor-NIH. J. Biomol. NMR 28, 249–261 (2004). · doi:10.1023/b:jnmr.0000013703.30623.f7
- Tjandra, N., Garrett, D. S., Gronenborn, A. M., Bax, A. & Clore, G. M. Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy. Nat. Struct. Biol. 4, 443–449 (1997). · DOI · Paper page
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Tai, M. D. S., Ochoa, L., Flydal, M. I., Velasco-Carneros, L., Muntaner, J., Santiago, C., Gamiz-Arco, G., Moro, F., Jung-KC, K., Gil-Cantero, D., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57733-6 · Cited by 16
Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins
Basciu, A., Athar, M., Kurt, H., Neville, C., Malloci, G., Muredda, F. C., Bosin, A., Ruggerone, P., Bonvin, A. M. J. J., & Vargiu, A. V. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c01810 · Cited by 12
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Devantier, K., Toft-Bertelsen, T. L., Prestel, A., Kjær, V. M. S., Sahin, C., Giulini, M., Louka, S., Spiess, K., Manandhar, A., Qvortrup, K., et al. (2025) · Science Advances · doi:10.1126/sciadv.ads3071 · Cited by 8
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Metadata
- Authors
- 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.
- Venue
- Nature Protocols
- Published
- 2024-06-17
- Volume
- 19
- Issue
- 11
- Pages
- 3219-3241
- ISSN
- 1750-2799 (ISSN-L)
- 1754-2189
- OpenAlex
- W4399731408
- Cited by
- 618
- References
- 15
- FWCI
- 71.80
- Type
- journal article
- Language
- en
- Open access
- green
- Licence
- www.springernature.com/gp/researchers/text-and-data-mining (tdm)
- www.springernature.com/gp/researchers/text-and-data-mining (vor)
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