Publications

Profile CV Publications In the media Research Teaching Ancillary activities In the media Contact

Areas of expertise

Research areas

Research ID: A-5420-2009

Scopus Author ID: 7003870500

Highlighted publications

Kastritis, P. L., Garcia Lopes Maia Rodrigues, J., Folkers, G. E., Boelens, R., & Bonvin, A. M. J. J. (2014). Proteins feel more than they see: Fine-tuning of binding affinity by properties of the non-interacting surface. Journal of Molecular Biology, 426(14), 2632-2652. https://doi.org/10.1016/j.jmb.2014.04.017

Kastritis, P., & Bonvin, A. M. J. J. (2013). Molecular origins of binding affinity: Seeking the Archimedean point. Current Opinion in Structural Biology, 23, 868-877. https://doi.org/10.1016/j.sbi.2013.07.001

Rosato, A., Aramini, J. M., van der Schot, G., de Vries, S. J., & Bonvin, A. M. J. J. (2012). Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data. Structure, 20(2), 227-236. https://doi.org/10.1016/j.str.2012.01.002

Karaca, E., & Bonvin, A. M. J. J. (2011). A Multidomain Flexible Docking Approach to Deal with Large Conformational Changes in the Modeling of Biomolecular Complexes. Structure, 19(3), 555-565. https://doi.org/10.1016/j.str.2011.01.014

Kastritis, P., & Bonvin, A. M. J. J. (2010). Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark. Journal of Proteome Research, 9, 2216-2225. https://doi.org/10.1021/pr9009854
https://dspace.library.uu.nl/bitstream/handle/1874/202590/Are-scoring-functions-in-protein_2010_Journal-of-Proteome-Research.pdf?sequence=1

Koukos, P. I., Xue, L. C., & Bonvin, A. M. J. J. (2019). Protein-ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3. Journal of Computer-Aided Molecular Design, 33(1), 83-91. https://doi.org/10.1007/s10822-018-0148-4

van Dijk, M., van Dijk, A. D. J., Hsu, V. L. H., Boelens, R., & Bonvin, A. M. J. J. (2006). Information-driven protein–DNA docking using HADDOCK: it is a matter of flexibility. Nucleic Acids Research, 34(11), 3317-3325. https://doi.org/10.1093/nar/gkl412

Dominguez, C., Boelens, R., & Bonvin, A. M. J. J. (2003). HADDOCK: a protein−protein docking approach based on biochemical or biophysical Information. Journal of the American Chemical Society, 125(7), 1731-1737. https://doi.org/10.1021/ja026939x

Hopf, T. A., Schaefe, C. P. I., Garcia Lopes Maia Rodrigues, J., Green, A. G., Kohlbacher, O., Sander, C., Bonvin, A. M. J. J., & Marks, D. S. (2014). Sequence co-evolution gives 3D contacts and structures of protein complexes. eLife, 3, [e03430]. https://doi.org/10.7554/eLife.03430

Vangone, A., & Bonvin, A. M. J. J. (2015). Contacts-based prediction of binding affinity in protein–protein complexes. eLife, 4, [e07454]. https://doi.org/10.7554/eLife.07454

de Vries, S. J., & Bonvin, A. M. J. J. (2008). How proteins get in touch: interface prediction in the study of biomolecular complexes. Current Protein and Peptide Science, 9(4), 394-406.
https://dspace.library.uu.nl/bitstream/handle/1874/33235/542.pdf?sequence=1

Karaca, E., Melquiond, A. S. J., de Vries, S. J., Kastritis, P., & Bonvin, A. M. J. J. (2010). Building macromolecular assemblies by information-driven docking: Introducing the haddock multibody docking server. Molecular & Cellular Proteomics, 9(8), 1784-1794. https://doi.org/10.1074/ mcp.M000051-MCP201
https://dspace.library.uu.nl/bitstream/handle/1874/202589/Mol%2520Cell%2520Proteomics-2010-Karaca-mcp.M000051-MCP201.pdf?sequence=3

de Vries, S. J., van Dijk, M., & Bonvin, A. M. J. J. (2010). The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, 5(5), 883-897. https://doi.org/10.1038/nprot.2010.32

Kalodimos, C., Biris, N., Bonvin, A. M. J. J., Levandoski, M. M., Guennuegues, M., Boelens, R., & Kaptein, R. (2004). Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science, 305(5682), 386-389. https://doi.org/10.1126/science.1097064

Schneider, T., Kruse, T., Wimmer, R., Wiedemann, I., Sass, V., Pag, U., Jansen, A., Nielsen, A. K., Mygind, P. H., Raventós, D. S., Neve, S., Ravn, B., Bonvin, A. M. J. J., De Maria, L., Andersen, A. S., Gammelgaard, L. K., Sahl, H-G., & Kristensen, H. -H. (2010). Plectasin, a fungal defensin, targets the bacterial cell wall precursor lipid II. Science, 328(5982), 1168-1172. https://doi.org/10.1126/science.1185723

Bonvin, A. M. J. J. (2006). Flexible protein–protein docking. Current Opinion in Structural Biology, 16, 194-200. https://doi.org/10.1016/j.sbi.2006.02.002

Weingarth, M. H., Ader, C., Melquiond, A. S. J., Nand, D., Pongs, O., Becker, S., Bonvin, A. M. J. J., & Baldus, M. (2012). Supramolecular structure of membrane-associated polypeptides by combining solid-state NMR and Molecular Dynamics simulations. Biophysical Journal, 103(1), 29-37. https://doi.org/10.1016/j.bpj.2012.05.016

Ambrosetti, F., Jiménez-García, B., Roel-Touris, J., & Bonvin, A. M. J. J. (2020). Modeling Antibody-Antigen Complexes by Information-Driven Docking. Structure with Folding & design, 28(1), 119-129.e2. https://doi.org/10.1016/j.str.2019.10.011
https://dspace.library.uu.nl/bitstream/handle/1874/392094/1_s2.0_S0969212619303521_main.pdf?sequence=1

Karaca, E., Garcia Lopes Maia Rodrigues, J., Graziadei, A., Bonvin, A. M. J. J., & Carlomagno, T. (2017). M3: an integrative framework for structure determination of molecular machines. Nature Methods, 14(9), 897-902. https://doi.org/10.1038/nmeth.4392

Wassenaar, T. A., van Dijk, M., Loureiro-Ferreira, N., van der Schot, G., de Vries, S. J., Schmitz, C. P. F., van der Zwan, J., Boelens, R., & Bonvin, A. M. J. J. (2011). WeNMR: structural biology on the grid. In G. Terstyanszky, & T. Kiss (Eds.), IWSG-Life 2011: Science Gateways for Life Sciences 2011
https://dspace.library.uu.nl/bitstream/handle/1874/234906/paper4.pdf?sequence=2

Garcia Lopes Maia Rodrigues, J., & Bonvin, A. M. J. J. (2014). Integrative computational modeling of protein interactions. The FEBS journal, 281(8), 1988-2003. https://doi.org/10.1111/febs.12771

2023

Scholarly publications

Jung, Y., Geng, C., Bonvin, A. M. J. J., Xue, L. C., & Honavar, V. G. (2023). MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein-Protein Docking Conformations. Biomolecules, 13(1). https://doi.org/10.3390/biom13010121

Jung, Y., Geng, C., Bonvin, A. M. J. J., Xue, L. C., & Honavar, V. G. (2023). MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein–Protein Docking Conformations. Biomolecules. https://doi.org/10.3390/biom13010121

Réau, M., Renaud, N., Xue, L. C., & Bonvin, A. M. J. J. (2023). DeepRank-GNN: A Graph Neural Network Framework to Learn Patterns in Protein-Protein Interfaces. Bioinformatics, 39(1), 1-8. [btac759]. https://doi.org/10.1093/bioinformatics/btac759

Ambrosetti, F., Jandova, Z., & Bonvin, A. M. J. J. (2023). Information-Driven Antibody-Antigen Modelling with HADDOCK. Methods in Molecular Biology, 2552, 267-282. https://doi.org/https://arxiv.org/abs/2005.03283, https://doi.org/10.1007/978-1-0716-2609-2_14

2022

Scholarly publications

Keulen, S. C. V., & Bonvin, A. M. J. J. (2022). Improving the Quality of Co-evolution Intermolecular Contact Prediction with DisVis. (pp. 1-22). bioRxiv. https://doi.org/10.1101/2022.11.03.515006

Madsen, M. S., Broekema, M. F., Madsen, M. R., Koppen, A., Borgman, A., Gräwe, C., Thomsen, E. G. K., Westland, D., Kranendonk, M. E. G., Koerkamp, M. G., Hamers, N., Bonvin, A. M. J. J., Pittol, J. M. R., Natarajan, K. N., Kersten, S., Holstege, F. C. P., Monajemi, H., van Mil, S. W. C., Vermeulen, M., ... Kalkhoven, E. (2022). PPARγ lipodystrophy mutants reveal intermolecular interactions required for enhancer activation. Nature Communications, 13(1), 1-19. [7090]. https://doi.org/10.1038/s41467-022-34766-9

Basciu, A., Callea, L., Motta, S., Bonvin, A. M. J. J., Bonati, L., & Vargiu, A. V. (2022). No dance, no partner! A tale of receptor flexibility in docking and virtual screening. In J. Caballero (Ed.), Virtual Screening and Drug Docking (pp. 43-97). (Annual Reports in Medicinal Chemistry; Vol. 59). Academic Press Inc.. https://doi.org/10.1016/bs.armc.2022.08.006

Rosário-Ferreira, N., Bonvin, A. M. J. J., & Moreira, I. S. (2022). Using machine-learning-driven approaches to boost hot-spot's knowledge. Wiley Interdisciplinary Reviews: Computational Molecular Science, 12(5), 1-25. [e1602]. https://doi.org/10.1002/wcms.1602

Charitou, V., Van Keulen, S. C., & Bonvin, A. M. J. J. (2022). Cyclization and Docking Protocol for Cyclic Peptide-Protein Modeling Using HADDOCK2.4. Journal of Chemical Theory and Computation, 18(6), 4027-4040. https://doi.org/10.1021/acs.jctc.2c00075

GEN-COVID Multicenter Study (2022). Pathogen-sugar interactions revealed by universal saturation transfer analysis. Science, 377(6604), 1-18. https://doi.org/10.1126/science.abm3125

Shukla, R., Lavore, F., Maity, S., Derks, M. G. N., Jones, C. R., Vermeulen, B. J. A., Melcrová, A., Morris, M. A., Becker, L. M., Wang, X., Kumar, R., Medeiros-Silva, J., van Beekveld, R. A. M., Bonvin, A. M. J. J., Lorent, J. H., Lelli, M., Nowick, J. S., MacGillavry, H. D., Peoples, A. J., ... Weingarth, M. (2022). Teixobactin kills bacteria by a two-pronged attack on the cell envelope. Nature, 608(7922), 390-396. https://doi.org/10.1038/s41586-022-05019-y

Garofalo, B., Bonvin, A. M. J. J., Bosin, A., Di Giorgio, F. P., Ombrato, R., & Vargiu, A. V. (2022). Molecular Insights Into Binding and Activation of the Human KCNQ2 Channel by Retigabine. Frontiers in Molecular Biosciences, 9, 1-14. [839249]. https://doi.org/10.3389/fmolb.2022.839249

Neijenhuis, T., van Keulen, S. C., & Bonvin, A. M. J. J. (2022). Interface refinement of low- to medium-resolution Cryo-EM complexes using HADDOCK2.4. Structure, 30(4), 476-484.e3. https://doi.org/10.1016/j.str.2022.02.001

Charitou, V., Keulen, S. C. V., & Bonvin, A. M. J. J. (2022, Jan 23). A Cyclisation and Docking Protocol for Cyclic Peptide-Protein Modelling using HADDOCK2.4. https://doi.org/10.1101/2022.01.21.477251

2021

Scholarly publications

Basciu, A., Vargiu, A. V., Malloci, G., Ruggerone, P., & Bonvin, A. M. (2021). In Silico Generation of Holo-Like Conformations of Very Flexible Allosteric Proteins Bearing Multiple Binding Sites. Biophysical Journal, 120(3), 115A-116A.

Bonvin, A. M. J. J. (2021). 50 years of PDB: a catalyst in structural biology. Nature Methods. https://doi.org/10.1038/s41592-021-01138-y

Renaud, N., Geng, C., Georgievska, S., Ambrosetti, F., Ridder, L., Marzella, D. F., Réau, M. F., Bonvin, A. M. J. J., & Xue, L. C. (2021). DeepRank: a deep learning framework for data mining 3D protein-protein interfaces. Nature Communications, 12(1), 1-8. [7068]. https://doi.org/10.1038/s41467-021-27396-0

Salo-Ahen, O. M. H., Alanko, I., Bhadane, R., Alexandre, A. M., Honorato, R. V., Hossain, S., Juffer, A. H., Kabedev, A., Lahtela-Kakkonen, M., Larsen, A. S., Lescrinier, E., Marimuthu, P., Mirza, M. U., Mustafa, G., Nunes-Alves, A., Pantsar, T., Saadabadi, A., Singaravelu, K., & Vanmeert, M. (2021). Molecular dynamics simulations in drug discovery and pharmaceutical development. Processes, 9(1), 1-60. [71]. https://doi.org/10.3390/pr9010071

Bonvin, A. M. J. J. (2021). 50 years of PBD: a catalyst in structural biology. Nature Methods, 18(5), 448-449. https://doi.org/10.1038/s41592-021-01138-y

Nizamuddin, S., Koidl, S., Bhuiyan, T., Werner, T. V., Biniossek, M. L., Bonvin, A. M. J. J., Lassmann, S., & Timmers, H. (2021). Integrating quantitative proteomics with accurate genome profiling of transcription factors by greenCUT&RUN. Nucleic Acids Research, 49(9), 1-18. [E49]. https://doi.org/10.1093/nar/gkab038

van Noort, C. W., Honorato, R. V., & Bonvin, A. M. J. J. (2021). Information-driven modeling of biomolecular complexes. Current Opinion in Structural Biology, 70, 70-77. https://doi.org/10.1016/j.sbi.2021.05.003

Honorato, R. V., Koukos, P. I., Jiménez-García, B., Tsaregorodtsev, A., Verlato, M., Giachetti, A., Rosato, A., & Bonvin, A. M. J. J. (2021). Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem. Frontiers in Molecular Biosciences, 8, 1-7. [729513]. https://doi.org/10.3389/fmolb.2021.729513

Jandova, Z., Vargiu, A. V., & Bonvin, A. M. J. J. (2021). Native or Non-Native Protein-Protein Docking Models? Molecular Dynamics to the Rescue. Journal of Chemical Theory and Computation, 17(9), 5944-5954. https://doi.org/10.1021/acs.jctc.1c00336

Koukos, P. I., Réau, M., & Bonvin, A. M. J. J. (2021). Shape-Restrained Modeling of Protein-Small-Molecule Complexes with High Ambiguity Driven DOCKing. Journal of Chemical Information and Modeling, 61(9), 4807-4818. https://doi.org/10.1021/acs.jcim.1c00796

Lensink, M. F., Brysbaert, G., Mauri, T., Nadzirin, N., Velankar, S., Chaleil, R. A. G., Clarence, T., Bates, P. A., Kong, R., Liu, B., Yang, G., Liu, M., Shi, H., Lu, X., Chang, S., Roy, R. S., Quadir, F., Liu, J., Cheng, J., ... Wodak, S. J. (2021). Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins: Structure, Function and Bioinformatics, 89(12), 1800-1823. https://doi.org/10.1002/prot.26222

Dudas, G., Hong, S. L., Potter, B. I., Calvignac-Spencer, S., Niatou-Singa, F. S., Tombolomako, T. B., Fuh-Neba, T., Vickos, U., Ulrich, M., Leendertz, F. H., Khan, K., Huber, C., Watts, A., Olendraitė, I., Snijder, J., Wijnant, K. N., Bonvin, A. M. J. J., Martres, P., Behillil, S., ... Baele, G. (2021). Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Nature Communications, 12(1), 1-12. [5769]. https://doi.org/10.1038/s41467-021-26055-8

le Paige, U. B., Xiang, S., Hendrix, M. M. R. M., Zhang, Y., Folkers, G. E., Weingarth, M., Bonvin, A. M. J. J., Kutateladze, T. G., Voets, I. K., Baldus, M., & van Ingen, H. (2021). Characterization of nucleosome sediments for protein interaction studies by solid-state NMR spectroscopy. Magnetic Resonance, 2(1), 187-202. https://doi.org/10.5194/mr-2-187-2021

Matos-Filipe, P., Preto, A. J., Koukos, P. I., Mourão, J., Bonvin, A. M. J. J., & Moreira, I. S. (2021). MENSAdb: a thorough structural analysis of membrane protein dimers. Database : the journal of biological databases and curation, 2021, [baab013]. https://doi.org/10.1093/database/baab013

Jiménez-García, B., Teixeira, J. M. C., Trellet, M., Rodrigues, J. P. G. L. M., & Bonvin, A. M. J. J. (2021). PDB-tools web: A user-friendly interface for the manipulation of PDB files. Proteins: Structure, Function and Genetics, 89(3), 330-335. https://doi.org/10.1002/prot.26018

2020

Scholarly publications

Orengo, C., Velankar, S., Wodak, S., Zoete, V., Bonvin, A. M. J. J., Elofsson, A., Feenstra, K. A., Gerloff, D. L., Hamelryck, T., Hancock, J. M., Helmer-Citterich, M., Hospital, A., Orozco, M., Perrakis, A., Rarey, M., Soares, C., Sussman, J. L., Thornton, J. M., Tuffery, P., ... Schneider, B. (2020). A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community) [version 1; peer review: 1 approved, 3 approved with reservations]. F1000Research. https://doi.org/10.12688/f1000research.20559.1

Saponaro, A., Maione, V., Bonvin, A., & Cantini, F. (2020). Understanding Docking Complexes of Macromolecules Using HADDOCK: The Synergy between Experimental Data and Computations. Bio-protocol, 10(20). https://doi.org/10.21769/bioprotoc.3793

Roel-Touris, J., Jiménez-García, B., & Bonvin, A. M. J. J. (2020). Integrative modeling of membrane-associated protein assemblies. Nature Communications, 11(1), [6210]. https://doi.org/10.1038/s41467-020-20076-5

Schwarz, M., Skrinjar, P., Fink, M. J., Kronister, S., Mechtler, T., Koukos, P. I., Bonvin, A. M. J. J., Kasper, D. C., & Mikula, H. (2020). A click-flipped enzyme substrate boosts the performance of the diagnostic screening for Hunter syndrome. Chemical Science, 11(47), 12671-12676. https://doi.org/10.1039/d0sc04696e

Lau, C. Y. J., Fontana, F., Mandemaker, L. D. B., Wezendonk, D., Vermeer, B., Bonvin, A. M. J. J., de Vries, R., Zhang, H., Remaut, K., van den Dikkenberg, J., Medeiros-Silva, J., Hassan, A., Perrone, B., Kuemmerle, R., Gelain, F., Hennink, W. E., Weingarth, M., & Mastrobattista, E. (2020). Author Correction: Control over the fibrillization yield by varying the oligomeric nucleation propensities of self-assembling peptides. Communications Chemistry, 3(1), [179]. https://doi.org/10.1038/s42004-020-00436-4

Lau, C. Y. J., Fontana, F., Mandemaker, L. D. B., Wezendonk, D., Vermeer, B., Bonvin, A. M. J. J., De Vries, R., Zhang, H., Remaut, K., Van Den Dikkenberg, J., Medeiros-silva, J., Hassan, A., Perrone, B., Kuemmerle, R., Gelain, F., Hennink, W. E., Weingarth, M., & Mastrobattista, E. (2020). Control over the fibrillization yield by varying the oligomeric nucleation propensities of self-assembling peptides. Communications Chemistry, 3(1), [164]. https://doi.org/10.1038/s42004-020-00417-7

Leitner, A., Bonvin, A. M. J. J., Borchers, C. H., Chalkley, R. J., Chamot-Rooke, J., Combe, C. W., Cox, J., Dong, M-Q., Fischer, L., Götze, M., Gozzo, F. C., Heck, A. J. R., Hoopmann, M. R., Huang, L., Ishihama, Y., Jones, A. R., Kalisman, N., Kohlbacher, O., Mechtler, K., ... Rappsilber, J. (2020). Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry. Structure, 28(11), 1259-1268. https://doi.org/10.1016/j.str.2020.09.011

Ambrosetti, F., Olsen, T. H., Olimpieri, P. P., Jiménez-García, B., Milanetti, E., Marcatilli, P., & Bonvin, A. M. J. J. (2020). proABC-2: PRediction Of AntiBody Contacts v2 and its application to information-driven docking. Bioinformatics, 36(20), 5107-5108. https://doi.org/10.1093/bioinformatics/btaa644

Roel-Touris, J., & Bonvin, A. M. J. J. (2020). Coarse-grained (hybrid) integrative modeling of biomolecular interactions. Computational and Structural Biotechnology Journal, 18, 1182-1190. https://doi.org/10.1016/j.csbj.2020.05.002

Palermo, G., Bonvin, A. M. J. J., Dal Peraro, M., Amaro, R. E., & Tozzini, V. (2020). Editorial: Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations. Frontiers in Molecular Biosciences, 7, [194]. https://doi.org/10.3389/fmolb.2020.00194

Rabouw, H. H., Visser, L. J., Passchier, T. C., Langereis, M. A., Liu, F., Giansanti, P., van Vliet, A. L. W., Dekker, J. G., van der Grein, S. G., Saucedo, J. G., Anand, A. A., Trellet, M. E., Bonvin, A. M. J. J., Walter, P., Heck, A. J. R., de Groot, R. J., & van Kuppeveld, F. J. M. (2020). Inhibition of the integrated stress response by viral proteins that block p-eIF2-eIF2B association. Nature Microbiology, 5, 1361-1373. https://doi.org/10.1038/s41564-020-0759-0

Shukla, R., Medeiros-Silva, J., Parmar, A., Vermeulen, B. J. A., Das, S., Paioni, A. L., Jekhmane, S., Lorent, J., Bonvin, A. M. J. J., Baldus, M., Lelli, M., Veldhuizen, E. J. A., Breukink, E., Singh, I., & Weingarth, M. (2020). Mode of action of teixobactins in cellular membranes. Nature Communications, 11(1), 2848. https://doi.org/10.1038/s41467-020-16600-2

Orengo, C., Velankar, S., Wodak, S., Zoete, V., Bonvin, A. M. J. J., Elofsson, A., Feenstra, K. A., Gerloff, D. L., Hamelryck, T., Hancock, J. M., Helmer-Citterich, M., Hospital, A., Orozco, M., Perrakis, A., Rarey, M., Soares, C., Sussman, J. L., Thornton, J. M., Tuffery, P., ... Schneider, B. (2020). A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). F1000Research, 9, [278]. https://doi.org/10.12688/f1000research.20559.1

Renaud, N., Jung, Y., Honavar, V., Geng, C., Bonvin, A. M. J. J., & Xue, L. C. (2020). iScore: An MPI supported software for ranking protein–protein docking models based on a random walk graph kernel and support vector machines. SoftwareX, 11, [100462]. https://doi.org/10.1016/j.softx.2020.100462

Trellet, M., van Zundert, G., & Bonvin, A. M. J. J. (2020). Protein–Protein Modeling Using Cryo-EM Restraints. In Z. Gáspári (Ed.), Structural Bioinformatics: Methods and Protocols (pp. 145-162). (Methods in Molecular Biology; Vol. 2112). Humana Press. https://doi.org/10.1007/978-1-0716-0270-6_11

Elez, K., Bonvin, A. M. J. J., & Vangone, A. (2020). Biological vs. Crystallographic protein interfaces: An overview of computational approaches for their classification. Crystals, 10(2), [114]. https://doi.org/10.3390/cryst10020114

Koukos, P. I., Roel-Touris, J., Ambrosetti, F., Geng, C., Schaarschmidt, J., Trellet, M. E., Melquiond, A. S. J., Xue, L. C., Honorato, R. V., Moreira, I., Kurkcuoglu, Z., Vangone, A., & Bonvin, A. M. J. J. (2020). An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45. Proteins: Structure, Function and Genetics. https://doi.org/10.1002/prot.25869

Koukos, P. I., & Bonvin, A. M. J. J. (2020). Integrative modelling of biomolecular complexes. Journal of Molecular Biology, 432(9), 2861-2881. https://doi.org/10.1016/j.jmb.2019.11.009

Basciu, A., Koukos, P. I., Malloci, G., Bonvin, A. M. J. J., & Vargiu, A. V. (2020). Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4. Journal of Computer-Aided Molecular Design, 34(2), 149–162. https://doi.org/10.1007/s10822-019-00244-6

Norman, R. A., Ambrosetti, F., Bonvin, A. M. J. J., Colwell, L. J., Kelm, S., Kumar, S., & Krawczyk, K. (2020). Computational approaches to therapeutic antibody design: established methods and emerging trends. Briefings in Bioinformatics, 21(5), 1549–1567. https://doi.org/10.1093/bib/bbz095

Roel-Touris, J., Bonvin, A. M. J. J., & Jiménez-García, B. (2020). LightDock goes information-driven. Bioinformatics, 36(3), 950–952. https://doi.org/10.1093/bioinformatics/btz642

Geng, C., Jung, Y., Renaud, N., Honavar, V., Bonvin, A. M. J. J., & Xue, L. C. (2020). iScore: A novel graph kernel-based function for scoring protein-protein docking models. Bioinformatics, 36(1), 112–121. https://doi.org/10.1093/bioinformatics/btz496

Lawson, T., El-Kamand, S., Boucher, D., Duong, D. C., Kariawasam, R., Bonvin, A. M. J. J., Richard, D. J., Gamsjaeger, R., & Cubeddu, L. (2020). The structural details of the interaction of single-stranded DNA binding protein hSSB2 (NABP1/OBFC2A) with UV-damaged DNA. Proteins: Structure, Function and Bioinformatics, 88(2), 319-326. https://doi.org/10.1002/prot.25806

Kurkcuoglu, Z., & Bonvin, A. M. J. J. (2020). Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems. Proteins: Structure, Function and Bioinformatics, 88(2), 292-306. https://doi.org/10.1002/prot.25802

2019

Scholarly publications

Broekema, M. F., Madsen, M. S., Madsen, M. R., Koppen, A., Kranendonk, M. E. G., Koerkamp, M. G., Hamers, N., Borgmans, A., Bonvin, A. M. J. J., Holstege, F. C. P., Spiering, W., Monajemi, H., Cassiman, D., Mandrup, S., & Kalkhoven, E. (2019). FPLD3-associated PPAR gamma mutants define subclasses of target genes. European Journal of Human Genetics, 27, 1339-1340.

Goldbach, L., Vermeulen, B. J. A., Caner, S., Liu, M., Tysoe, C., van Gijzel, L., Yoshisada, R., Trellet, M., van Ingen, H., Brayer, G. D., Bonvin, A. M. J. J., & Jongkees, S. A. K. (2019). Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic alpha-Amylase. ACS Chemical Biology, 14(8), 1751-1759. https://doi.org/10.1021/acschembio.9b00290

Geng, C., Xue, L. C., Roel-Touris, J., & Bonvin, A. M. J. J. (2019). Finding the Delta Delta G spot: Are predictors of binding affinity changes upon mutations in protein-protein interactions ready for it? Wiley Interdisciplinary Reviews: Computational Molecular Science, 9(5). https://doi.org/10.1002/wcms.1410

Berman, H. M., Adams, P. D., Bonvin, A., Burley, S. K., Carragher, B., Chiu, W., Dimaio, F., Ferrin, T. E., Gabanyi, M. J., Goddard, T. D., Griffin, P. R., Haas, J., Hanke, C. A., Hoch, J. C., Hummer, G., Kurisu, G., Lawson, C. L., Leitner, A., & Markley, J. L. (2019). Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure/Folding and Design, 27(12), 1745-1759. https://doi.org/10.1016/j.str.2019.11.002

CASP-CAPRI (2019). Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment. Proteins: Structure, Function and Genetics, 87(12), 1200-1221. https://doi.org/10.1002/prot.25838

Ambrosetti, F., Jiménez-García, B., Roel-Touris, J., & Bonvin, A. M. J. J. (2019). Information-Driven Modelling of Antibody-Antigen Complexes. SSRN Electronic Journal. https://doi.org/10.2139/ssrn.3362436

Jiménez-García, B., Elez, K., Koukos, P. I., Bonvin, A. M., & Vangone, A. (2019). PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes. Bioinformatics, 35(22), 4821–4823. https://doi.org/10.1093/bioinformatics/btz437

Abraham, M. J., Apostolov, R. P., Barnoud, J., Bauer, P., Blau, C., Bonvin, A. M. J. J., Chavent, M., Chodera, J. D., Čondić-Jurkić, K., Delemotte, L., Grubmüller, H., Howard, R. J., Jordan, E. J., Lindal, E., Ollila, O. H. S., Selent, J., Smith, D. G. A., Stansfeld, P. J., Tiemann, J. K. S., ... Zhmurov, A. (2019). Sharing Data from Molecular Simulations. Journal of Chemical Information and Modeling, 59(10), 4093-4099. https://doi.org/10.1021/acs.jcim.9b00665

Honorato, R. V., Roel-Touris, J., & Bonvin, A. M. J. J. (2019). MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing. Frontiers in Molecular Biosciences, 6. https://doi.org/10.3389/fmolb.2019.00102

Morris, C., Andreetto, P., Banci, L., Bonvin, A. M. J. J., Chojnowski, G., Cano, L. D., Carazo, J. M., Conesa, P., Daenke, S., Damaskos, G., Giachetti, A., Haley, N. E. C., Hekkelman, M. L., Heuser, P., Joosten, R. P., Kouřil, D., Křenek, A., Kulhánek, T., Lamzin, V. S., ... Winn, M. (2019). West-Life: A Virtual Research Environment for structural biology. Journal of Structural Biology: X, 1, [100006]. https://doi.org/10.1016/j.yjsbx.2019.100006

Vangone, A., Schaarschmidt, J., Koukos, P., Geng, C., Citro, N., Trellet, M. E., Xue, L. C., & Bonvin, A. M. J. J. (2019). Large-scale prediction of binding affinity in protein-small ligand complexes: The PRODIGY-LIG web server. Bioinformatics, 35(9), 1585-1587. https://doi.org/10.1093/bioinformatics/bty816

Basciu, A., Malloci, G., Pietrucci, F., Bonvin, A. M. J. J., & Vargiu, A. V. (2019). Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape. Journal of Chemical Information and Modeling, 59(4), 1515-1528. https://doi.org/10.1021/acs.jcim.8b00730

Roel-Touris, J., Don, C. G., V. Honorato, R., Rodrigues, J. P. G. L. M., & Bonvin, A. M. J. J. (2019). Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK. Journal of Chemical Theory and Computation, 15, 6358−6367. https://doi.org/10.1021/acs.jctc.9b00310

Goldbach, L., Vermeulen, B. J. A., Caner, S., Liu, M., Tysoe, C., van Gijzel, L., Yoshisada, R., Trellet, M., van Ingen, H., Brayer, G. D., Bonvin, A. M. J. J., & Jongkees, S. A. K. (2019). Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic α-Amylase. ACS Chemical Biology, 14(8), 1751-1759. https://doi.org/10.1021/acschembio.9b00290

Geng, C., Xue, L. C., Roel-Touris, J., & Bonvin, A. M. J. J. (2019). Finding the ΔΔG spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it? Wiley Interdisciplinary Reviews: Computational Molecular Science, 9(5), [e1410]. https://doi.org/10.1002/wcms.1410

Broekema, M. F., Massink, M. P. G., Donato, C., de Ligt, J., Schaarschmidt, J., Borgman, A., Schooneman, M. G., Melchers, D., Gerding, M. N., Houtman, R., Bonvin, A. M. J. J., Majithia, A. R., Monajemi, H., van Haaften, G. W., Soeters, M. R., & Kalkhoven, E. (2019). Natural helix 9 mutants of PPARγ differently affect its transcriptional activity. Molecular Metabolism, 20, 115-127. https://doi.org/10.1016/j.molmet.2018.12.005

Geng, C., Vangone, A., Folkers, G. E., Xue, L. C., & Bonvin, A. M. J. J. (2019). iSEE: Interface Structure, Evolution and Energy-based machine learning predictor of binding affinity changes upon mutations. Proteins: Structure, Function and Genetics, 87(2), 110-119. https://doi.org/10.1002/prot.25630

2018

Scholarly publications

Rodrigues, J. P. G. L. M., Teixeira, J. M. C., Trellet, M., & Bonvin, A. M. J. J. (2018). Pdb-tools: A swiss army knife for molecular structures [version 1; referees: 2 approved]. F1000Research, 2018(7), [1961]. https://doi.org/10.12688/f1000research.17456.1

Elez, K., Bonvin, A. M. J. J., & Vangone, A. (2018). Distinguishing crystallographic from biological interfaces in protein complexes: role of intermolecular contacts and energetics for classification. BMC Bioinformatics, 19, [438]. https://doi.org/10.1186/s12859-018-2414-9

Bonvin, A. M. J. J., Karaca, E., Kastritis, P. L., & Rodrigues, J. P. G. L. M. (2018). Defining distance restraints in HADDOCK. Nature Protocols, 13(7), [1503]. https://doi.org/10.1038/s41596-018-0017-6

Koukos, P. I., Faro, I., van Noort, C. W., & Bonvin, A. M. J. J. (2018). A Membrane Protein Complex Docking Benchmark. Journal of Molecular Biology, 430(24), 5246-5256. https://doi.org/10.1016/j.jmb.2018.11.005

Salomoni, D., Campos, I., Gaido, L., de Lucas, J. M., Solagna, P., Gomes, J., Matyska, L., Fuhrman, P., Hardt, M., Donvito, G., Dutka, L., Plociennik, M., Barbera, R., Blanquer, I., Ceccanti, A., Cetinic, E., David, M., Duma, C., López-García, A., ... Wegh, B. (2018). INDIGO-DataCloud: a Platform to Facilitate Seamless Access to E-Infrastructures. Journal of Grid Computing, 16(3), 381-408. https://doi.org/10.1007/s10723-018-9453-3

Roseboom, W., Nazir, M. G., Meiresonne, N. Y., Mohammadi, T., Verheul, J., Buncherd, H., Bonvin, A. M. J. J., de Koning, L. J., de Koster, C. G., De Jong, L., & Den Blaauwen, T. (2018). Mapping the contact sites of the escherichia coli division-initiating proteins FtsZ and ZapA by BAMG cross-linking and site-directed mutagenesis. International Journal of Molecular Sciences, 19(10), [2928]. https://doi.org/10.3390/ijms19102928

Preto, A. J., Almeida, J. G., Schaarschmidt, J., Xue, L. C., Moreira, I. S., & Bonvin, A. M. J. J. (2018). Computational Tools for the Structural Characterization of Proteins and Their Complexes from Sequence-Evolutionary Data. In R. A. Meyers (Ed.), Encyclopedia of Analytical Chemistry: Applications, Theory and Instrumentation (pp. 1-19). Wiley. https://doi.org/10.1002/9780470027318.a9615
https://dspace.library.uu.nl/bitstream/handle/1874/380927/EAC_preprint.pdf?sequence=1

Narasimhan, S., Mance, D., de Agrela Pinto, C., Weingarth, M., Bonvin, A. M. J. J., & Baldus, M. (2018). Rapid prediction of multi-dimensional NMR data sets using FANDAS. In R. Ghose (Ed.), Protein NMR: Methods and Protocols (pp. 111-132). (Methods in Molecular Biology; Vol. 1688). Humana Press. https://doi.org/10.1007/978-1-4939-7386-6_6

Kurkcuoglu Soner, Z., Koukos, P., Citro, N., Trellet, M. E., Garcia Lopes Maia Rodrigues, J., de Sousa Moreira, I., Roel-touris, J., Melquiond, A. S. J., Geng, C., Schaarschmidt, J., Xue, L. C., Vangone, A., & Bonvin, A. M. J. J. (2018). Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2. Journal of Computer-Aided Molecular Design, 32(1), 175-185. https://doi.org/10.1007/s10822-017-0049-y

2017

Scholarly publications

Vangone, A., & Bonvin, A. M. J. J. (2017). Prodigy: A Contact-based Predictor of Binding Affinity in Protein-protein Complexes. Bio-protocol, 7(3). https://doi.org/10.21769/BioProtoc.2124

Basciu, A., Pietrucci, F., Bonvin, A. M. J. J., & Vargiu, A. V. (2017). A new protocol to improve the predictive power of molecular docking. European Biophysics Journal, 46(1), 207. https://doi.org/10.1007/s00249-017-1222-x

Vangone, A., Garcia Lopes Maia Rodrigues, J., Xue, L. C., van Zundert, G. C. P., Geng, C., Kurkcuoglu Soner, Z., Nellen, M., Narasimhan, S., Karaca, E., van Dijk, M., Melquiond, A. S. J., Visscher, K. M., Trellet, M., Kastritis, P. L., & Bonvin, A. M. J. J. (2017). Erratum: Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1: HADDOCK in CASP-CAPRI Round 1 (Proteins: Structure, Function, and Bioinformatics, (2017), 85, 3, (417-423), 10.1002/prot.25198). Proteins: Structure, Function and Genetics, 85(8), 1589. https://doi.org/10.1002/prot.25339

Vangone, A., Oliva, R., Cavallo, L., & Bonvin, A. M. J. J. (2017). Prediction of Biomolecular Complexes. In D. J. Rigden (Ed.), From Protein Structure to Function with Bioinformatics (2 ed., pp. 265-292). Springer Science. https://doi.org/10.1007/978-94-024-1069-3_8

Schaarschmidt, J., Monastyrskyy, B., Kryshtafovych, A., & Bonvin, A. M. J. J. (2017). Assessment of contact predictions in CASP12: co-evolution and deep learning coming of age. Proteins: Structure, Function and Genetics, 86(S1), 51-66. https://doi.org/10.1002/prot.25407

de Sousa Moreira, I., Koukos, P., Melo, R., Almeida, J. G., Preto, A. J., Schaarschmidt, J., Trellet, M., Gümüş, Z. H., Costa, J., & Bonvin, A. M. J. J. (2017). SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots. Scientific Reports, 7(1), [8007]. https://doi.org/10.1038/s41598-017-08321-2

Almeida, J. G., Preto, A. J., Koukos, P., Bonvin, A. M. J. J., & de Sousa Moreira, I. (2017). Membrane proteins structures: A review on computational modeling tools. Biochimica et Biophysica Acta - Biomembranes, 1859(10), 2021-2039. https://doi.org/10.1016/j.bbamem.2017.07.008
https://dspace.library.uu.nl/bitstream/handle/1874/363472/BBA.pdf?sequence=2

Visscher, K. M., Medeiros-silva, J., Mance, D., Garcia Lopes Maia Rodrigues, J., Daniëls, M., Bonvin, A. M. J. J., Baldus, M., & Weingarth, M. (2017). Supramolecular Organization and Functional Implications of K+ Channel Clusters in Membranes. Angewandte Chemie-International Edition, 56(43), 13222-13227. https://doi.org/10.1002/anie.201705723

de Bruin, R. C. G., Stam, A. G. M., Vangone, A., van Bergen En Henegouwen, P. M. P., Verheul, H. M. W., Sebestyén, Z., Kuball, J., Bonvin, A. M. J. J., de Gruijl, T. D., & van der Vliet, H. J. (2017). Correction: Prevention of Vγ9Vδ2 T Cell Activation by a Vγ9Vδ2 TCR Nanobody. Journal of Immunology, 198(9), 3759. https://doi.org/10.4049/jimmunol.1700317

Geng, C., Narasimhan, S., Garcia Lopes Maia Rodrigues, J., & Bonvin, A. M. J. J. (2017). Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK. In O. Schueler-Furman, & N. London (Eds.), Modeling Peptide-Protein Interactions: Methods and Protocols (Vol. 1561, pp. 109-138). (Methods in Molecular Biology; Vol. 1561). Springer Science & Business Media, LLC. https://doi.org/10.1007/978-1-4939-6798-8_8

Vangone, A., Garcia Lopes Maia Rodrigues, J., Xue, L. C., van Zundert, G. C. P., Geng, C., Kurkcuoglu Soner, Z., Nellen, M., Narasimhan, S., Karaca, E., van Dijk, M., Melquiond, A. S. J., Visscher, K. M., Trellet, M., Kastritis, P. L., & Bonvin, A. M. J. J. (2017). Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1. Proteins: Structure, Function and Genetics, 85(3), 417–423. https://doi.org/10.1002/prot.25198

van Zundert, G. C. P., Trellet, M., Schaarschmidt, J., Kurkcuoglu Soner, Z., David, M., Verlato, M., Rosato, A., & Bonvin, A. M. J. J. (2017). The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes. Journal of Molecular Biology, 429(3), 399-407. https://doi.org/10.1016/j.jmb.2016.11.032
https://dspace.library.uu.nl/bitstream/handle/1874/348925/disvis.pdf?sequence=1

Xue, L. C., Garcia Lopes Maia Rodrigues, J., Dobbs, D., Honavar, V., & Bonvin, A. M. J. J. (2017). Template-based protein-protein docking exploiting pairwise interfacial residue restraints. Briefings in Bioinformatics, 18(3), 458-466. https://doi.org/10.1093/bib/bbw027

Bohnuud, T., Luo, L., Wodak, S. J., Bonvin, A. M. J. J., Weng, Z., Vajda, S., Schueler-Furman, O., & Kozakov, D. (2017). A benchmark testing ground for integrating homology modeling and protein docking. Proteins: Structure function and bioinformatics, 85(1), 10-17. https://doi.org/10.1002/prot.25063

2016

Scholarly publications

Grinter, R., Josts, I., Mosbahi, K., Roszak, A. W., Cogdell, R. J., Bonvin, A. M. J. J., Milner, J. J., Kelly, S. M., Byron, O., Smith, B. O., & Walker, D. (2016). Structure of the bacterial plant-ferredoxin receptor FusA. Nature Communications, 7, [13308]. https://doi.org/10.1038/ncomms13308

Felix, J., Kandiah, E., De Munck, S., Bloch, Y., Van Zundert, G. C. P., Pauwels, K., Dansercoer, A., Novanska, K., Read, R. J., Bonvin, A. M. J. J., Vergauwen, B., Verstraete, K., Gutsche, I., & Savvides, S. N. (2016). Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF. Nature Communications, 7, [13228]. https://doi.org/10.1038/ncomms13228

Xue, L., Garcia Lopes Maia Rodrigues, J., Kastritis, P. L., Bonvin, A. M., & Vangone, A. (2016). PRODIGY: a web server for predicting the binding affinity of protein-protein complexes. Bioinformatics, 32(23), 3676-3678. https://doi.org/10.1093/bioinformatics/btw514
https://dspace.library.uu.nl/bitstream/handle/1874/345622/PRODIGY_post_print.pdf?sequence=3

de Bruin, R. C. G., Stam, A. G. M., Vangone, A., van Bergen En Henegouwen, P. M. P., Verheul, H. M. W., Sebestyén, Z., Kuball, J., Bonvin, A. M. J. J., de Gruijl, T. D., & van der Vliet, H. J. (2016). Prevention of Vγ9Vδ2 T Cell Activation by a Vγ9Vδ2 TCR Nanobody. Journal of Immunology, 198, 308-317. https://doi.org/10.4049/jimmunol.1600948

Spiliotopoulos, D., Kastritis, P. L., Melquiond, A. S. J., Bonvin, A. M. J. J., Musco, G., Rocchia, W., & Spitaleri, A. (2016). dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking. Frontiers in Molecular Biosciences, 3, [46]. https://doi.org/10.3389/fmolb.2016.00046

Geng, C., Vangone, A., & Bonvin, A. M. J. J. (2016). Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes. Protein Engineering, Design & Selection, 29(8), 291-9. https://doi.org/10.1093/protein/gzw020
https://dspace.library.uu.nl/bitstream/handle/1874/337454/pre_print.pdf?sequence=3

Melo, R., Fieldhouse, R., Melo, A., Correia, J. D. G., Cordeiro, M. N. D. S., Gümüş, Z. H., Costa, J., Bonvin, A. M. J. J., & de Sousa Moreira, I. (2016). A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces. International Journal of Molecular Sciences, 17(8). https://doi.org/10.3390/ijms17081215

van Zundert, G. C. P., & Bonvin, A. M. J. J. (2016). Defining the limits and reliability of rigid-body fitting in cryo-EM maps using multi-scale image pyramids. Journal of Structural Biology, 195(2), 252-258. https://doi.org/10.1016/j.jsb.2016.06.011
https://dspace.library.uu.nl/bitstream/handle/1874/337452/vanZundert_post_print.pdf?sequence=3

Lensink, M. F., Velankar, S., Kryshtafovych, A., Huang, S. Y., Schneidman-Duhovny, D., Sali, A., Segura, J., Fernandez-Fuentes, N., Viswanath, S., Elber, R., Grudinin, S., Popov, P., Neveu, E., Lee, H., Baek, M., Park, S., Heo, L., Rie Lee, G., Seok, C., ... Wodak, S. J. (2016). Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins: Structure function and bioinformatics, 84(S1), 323-348. https://doi.org/10.1002/prot.25007

Meyer, P. A., Socias, S., Key, J., Ransey, E., Tjon, E. C., Buschiazzo, A., Lei, M., Botka, C., Withrow, J., Neau, D., Rajashankar, K., Anderson, K. S., Baxter, R. H., Blacklow, S. C., Boggon, T. J., Bonvin, A. M. J. J., Borek, D., Brett, T. J., Caflisch, A., ... Sliz, P. (2016). Data publication with the structural biology data grid supports live analysis. Nature Communications [E], 7, [10882]. https://doi.org/10.1038/ncomms10882

Liu, Y., Garcia Lopes Maia Rodrigues, J., Bonvin, A. M. J. J., Zaal, E. A., Berkers, C. R., Heger, M., Gawarecka, K., Swiezewska, E., Breukink, E., & Egmond, M. R. (2016). New insight into the catalytic mechanism of bacterial mray from enzyme kinetics and docking studies. Journal of Biological Chemistry, 291(29), 15057-15068. https://doi.org/10.1074/jbc.M116.717884

van Zundert, G. C. P., Garcia Lopes Maia Rodrigues, J., Trellet, M., Schmitz, C., Kastritis, P. L., Karaca, E., Melquiond, A. S. J., van Dijk, M., de Vries, S. J., & Bonvin, A. M. J. J. (2016). The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. Journal of Molecular Biology, 428(4), 720-725. https://doi.org/10.1016/j.jmb.2015.09.014

Kalia, M., Willkomm, S., Claussen, J. C., Restle, T., & Bonvin, A. M. J. J. (2016). Novel Insights into Guide RNA 5'-Nucleoside/Tide Binding by Human Argonaute 2. International Journal of Molecular Sciences, 17(1), [22]. https://doi.org/10.3390/ijms17010022

Garcia Lopes Maia Rodrigues, J., Melquiond, A. S. J., & Bonvin, A. M. J. J. (2016). Molecular dynamics characterization of the conformational landscape of small peptides: A series of hands-on collaborative practical sessions for undergraduate students. Biochemistry and Molecular Biology Education, 44(2), 160-167. https://doi.org/10.1002/bmb.20941
https://dspace.library.uu.nl/bitstream/handle/1874/344402/post_print.pdf?sequence=3

Jung, S., Fischer, J., Spudy, B., Kerkow, T., Sönnichsen, F. D., Xue, L., Bonvin, A. M. J. J., Goettig, P., Magdolen, V., Meyer-Hoffert, U., & Grötzinger, J. (2016). The solution structure of the kallikrein-related peptidases inhibitor SPINK6. Biochemical and Biophysical Research Communications, 471(1), 103-108. https://doi.org/10.1016/j.bbrc.2016.01.172

Zhang, R., Eckert, T., Lutteke, T., Hanstein, S., Scheidig, A., Bonvin, A. M. J. J., Nifantiev, N. E., Kozar, T., Schauer, R., Enani, M. A., & Siebert, H-C. (2016). Structure-Function Relationships of Antimicrobial Peptides and Proteins with Respect to Contact Molecules on Pathogen Surfaces. Current Topics in Medicinal Chemistry, 16(1), 89-98. https://doi.org/10.2174/1568026615666150703120753

Deplazes, E., Davies, J., Bonvin, A. M. J. J., King, G. F., & Mark, A. E. (2016). Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion Channel (ASIC) 1a. Journal of Chemical Information and Modeling, 56(1), 127-138. https://doi.org/10.1021/acs.jcim.5b00529
https://dspace.library.uu.nl/bitstream/handle/1874/344398/Deplazes_post_print.pdf?sequence=3

Other output

Kurkcuoglu Soner, Z., & Bonvin, A. M. J. J. (2016). Science in the clouds: Virtualizing HADDOCK, PowerFit and DisVis using INDIGO-DataCloud solutions. https://f1000research.com/posters/5-874
https://dspace.library.uu.nl/bitstream/handle/1874/351030/Cloud.pdf?sequence=1

Trellet, M. E., Schaarschmidt, J., van Zundert, G. C. P., Kurkcuoglu Soner, Z., Melquiond, A. S. J., & Bonvin, A. M. J. J. (2016). Integrative modelling goes HPC/HTC. https://f1000research.com/posters/5-2216

2015

Scholarly publications

Bern, M., Marino, F., Mommen, G. P. M., Leney, A. C., Bonvin, A. M. J. J., van Els, C. A. C. M., Becker, C., & Heck, A. J. R. (2015). Glycosylation on peptides presented by HLA class I molecules. Glycobiology, 25(11), 1248-1249.

C.p.van Zundert, G., & M.j.j. Bonvin, A. (2015). Fast and sensitive rigid-body fitting into cryo-EM density maps with PowerFit. AIMS Biophysics, 2(2), 73-87. https://doi.org/10.3934/biophy.2015.2.73

Brewer, K. D., Bacaj, T., Cavalli, A., Camilloni, C., Swarbrick, J. D., Liu, J., Zhou, A., Zhou, P., Barlow, N., Xu, J., Seven, A. B., Prinslow, E. A., Voleti, R., Häussinger, D., Bonvin, A. M. J. J., Tomchick, D. R., Vendruscolo, M., Graham, B., Südhof, T. C., & Rizo, J. (2015). Dynamic binding mode of a Synaptotagmin-1-SNARE complex in solution. Nature Structural and Molecular Biology, 22(7), 555-64. https://doi.org/10.1038/nsmb.3035

van Zundert, G. C. P., Melquiond, A. S. J., & Bonvin, A. M. J. J. (2015). Integrative Modeling of Biomolecular Complexes: HADDOCKing with Cryo-Electron Microscopy Data. Structure, 23(5), 949-60. https://doi.org/10.1016/j.str.2015.03.014

Duarte, A. M. S., Psomopoulos, F. E., Blanchet, C., Bonvin, A. M. J. J., Corpas, M., Franc, A., Jimenez, R. C., de Lucas, J. M., Nyrönen, T., Sipos, G., & Suhr, S. B. (2015). Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis. Frontiers in Genetics [E], 6, 197. https://doi.org/10.3389/fgene.2015.00197

Xue, L., Dobbs, D., Bonvin, A. M. J. J., & Honavar, V. (2015). Computational prediction of protein interfaces: A review of data driven methods. FEBS Letters, 589(23), 3516-26. https://doi.org/10.1016/j.febslet.2015.10.003

Bonvin, A. M., & Keskin, O. (2015). Editorial overview: Protein-protein interactions. Current Opinion in Structural Biology, 35, vii-ix. https://doi.org/10.1016/j.sbi.2015.11.004

Sali, A., Berman, H. M., Schwede, T., Trewhella, J., Kleywegt, G., Burley, S. K., Markley, J., Nakamura, H., Adams, P., Bonvin, A. M. J. J., Chiu, W., Peraro, M. D., Di Maio, F., Ferrin, T. E., Grünewald, K., Gutmanas, A., Henderson, R., Hummer, G., Iwasaki, K., ... Westbrook, J. D. (2015). Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure, 23(7), 1156-1167. [3197]. https://doi.org/10.1016/j.str.2015.05.013

Vreven, T., Moal, I. H., Vangone, A., Pierce, B. G., Kastritis, P. L., Torchala, M., Chaleil, R., Jiménez-García, B., Bates, P. A., Fernandez-Recio, J., Bonvin, A. M. J. J., & Weng, Z. (2015). Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. Journal of Molecular Biology, 427(19), 3031-3041. https://doi.org/10.1016/j.jmb.2015.07.016
https://dspace.library.uu.nl/bitstream/handle/1874/354214/Docking_Benchmark5_post_print.pdf?sequence=1

Van Zundert, G. C. P., & Bonvin, A. M. J. J. (2015). DisVis: Quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes. Bioinformatics, 31(19), 3222-3224. https://doi.org/10.1093/bioinformatics/btv333

Kaplan, M., Cukkemane, A., Van Zundert, G. C. P., Narasimhan, S., Daniëls, M., Mance, D., Waksman, G., Bonvin, A. M. J. J., Fronzes, R., Folkers, G. E., & Baldus, M. (2015). Probing a cell-embedded megadalton protein complex by DNP-supported solid-state NMR. Nature Methods, 12(7), 649-652. https://doi.org/10.1038/nmeth.3406

Vangone, A., & Bonvin, A. M. J. J. (2015). Contacts-based prediction of binding affinity in protein–protein complexes. eLife, 4, [e07454]. https://doi.org/10.7554/eLife.07454

Van Der Schot, G., & Bonvin, A. M. J. J. (2015). Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR. Journal of Biomolecular NMR, 62(4), 497-502. https://doi.org/10.1007/s10858-015-9942-7

Sinnige, T., Weingarth, M., Daniels, M., Boelens, R., Bonvin, A. M. J. J., Houben, K., & Baldus, M. (2015). Conformational Plasticity of the POTRA 5 Domain in the Outer Membrane Protein Assembly Factor BamA. Structure, 23(7), 1317-1324. https://doi.org/10.1016/j.str.2015.04.014

Marino, F., Bern, M., Mommen, G. P. M., Leney, A. C., van Gaans-van den Brink, J. A. M., Bonvin, A. M. J. J., Becker, C., van Els, C. A. C. M., & Heck, A. J. R. (2015). Extended O-GlcNAc on HLA Class-I-Bound Peptides. Journal of the American Chemical Society, 10922–10925. https://doi.org/10.1021/jacs.5b06586

Radmalekshahi, M., Visscher, K. M., Garcia Lopes Maia Rodrigues, J., De Vries, R., Hennink, W. E., Baldus, M., Bonvin, A. M. J. J., Mastrobattista, E., & Weingarth, M. (2015). The Supramolecular Organization of a Peptide-Based Nanocarrier at High Molecular Detail. Journal of the American Chemical Society, 137(24), 7775-7784. https://doi.org/10.1021/jacs.5b02919

Garcia Lopes Maia Rodrigues, J., Karaca, E., & Bonvin, A. M. J. J. (2015). Information-driven structural modelling of protein-protein interactions. In A. Kukol (Ed.), Molecular Modeling of Proteins (second edition ed., Vol. IV, pp. 399-424). (Methods in Molecular Biology; Vol. 1215). Humana Press. https://doi.org/10.1007/978-1-4939-1465-4_18

Vranken, W. F., Vuister, G. W., & Bonvin, A. M. J. J. (2015). NMR-based modeling and refinement of protein 3D structures. In Molecular Modeling of Proteins (pp. 351-380). (Methods in Molecular Biology; Vol. 1215). Humana Press. https://doi.org/10.1007/978-1-4939-1465-4_16

Trellet, M., Melquiond, A. S. J., & Bonvin, A. M. J. J. (2015). Information-driven modeling of protein-peptide complexes. Methods in Molecular Biology, 1268, 221-239. https://doi.org/10.1007/978-1-4939-2285-7_10

Visscher, K. M., Kastritis, P. L., & Bonvin, A. M. J. J. (2015). Non-interacting surface solvation and dynamics in protein-protein interactions. Proteins: Structure function and bioinformatics, 83(3), 445-458. https://doi.org/10.1002/prot.24741

Other output

Vangone, A., & Bonvin, A. M. J. J. (2015). HADDOCK docking models. SBGrid Data Bank. https://doi.org/10.15785/SBGRID/131

2014

Scholarly publications

Kalia, M., Willkomm, S., Claussen, J. C., Bonvin, A. M. J. J., & Restle, T. (2014). A Single Inter-Domain Salt Bridge within the Human Argonaute 2 Protein Crucially Affects Protein Folding and Consequently Enzymatic Activity. Biophysical Journal, 106(2, SUPPLEMENT 1), 26A-26A. https://doi.org/10.1016/j.bpj.2013.11.198

Varney, K. M., Bonvin, A. M. J. J., Pazgier, M., Malin, J., & Yu, W. (2014). Correction: Turning Defense into Offense: Defensin Mimetics as Novel Antibiotics Targeting Lipid II. PLoS Pathogens, 10(12), 1-1. [e1004611]. https://doi.org/10.1371/journal.ppat.1004611

van der Cruijsen, E., Visscher, K., Rodrigues, J., Bonvin, A., Baldus, M., & Weingarth, M. (2014). Ion Channel - Ion Channel Interaction at Atomic Resolution. Biophysical Journal, 106(2), 628a. https://doi.org/10.1016/j.bpj.2013.11.3474

Garcia Lopes Maia Rodrigues, J., & Bonvin, A. M. J. J. (2014). Integrative computational modeling of protein interactions. The FEBS journal, 281(8), 1988-2003. https://doi.org/10.1111/febs.12771

Kastritis, P. L., Garcia Lopes Maia Rodrigues, J., & Bonvin, A. M. J. J. (2014). HADDOCK_2P2I: A biophysical model for predicting the binding affinity of protein-protein interaction inhibitors. Journal of Chemical Information and Modeling, 54(3), 826-836. https://doi.org/10.1021/ci4005332

Ferguson, F. M., Dias, D. M., Garcia Lopes Maia Rodrigues, J., Wienk, H., Boelens, R., Bonvin, A. M. J. J., Abell, C., & Ciulli, A. (2014). Binding Hotspots of BAZ2B Bromodomain: Histone Interaction Revealed by Solution NMR Driven Docking. Biochemistry, 53(42), 6706-6716. https://doi.org/10.1021/bi500909d

Rey, M., Sarpe, V., Burns, K. M., Buse, J., Baker, C. A. H., van Dijk, M., Wordeman, L., Bonvin, A. M. J. J., & Schriemer, D. C. (2014). Mass Spec Studio for Integrative Structural Biology. Structure, 22(10), 1538-1548. https://doi.org/10.1016/j.str.2014.08.013

Van Ingen, H., & Bonvin, A. M. J. J. (2014). Information-driven modeling of large macromolecular assemblies using NMR data. Journal of Magnetic Resonance, 241(1), 103-114. https://doi.org/10.1016/j.jmr.2013.10.021

van Zundert, G. C. P., & Bonvin, A. M. J. J. (2014). Modeling protein-protein complexes using the HADDOCK webserver "modeling protein complexes with HADDOCK". In Protein Structure Prediction (pp. 163-179). (Methods in Molecular Biology; Vol. 1137). https://doi.org/10.1007/978-1-4939-0366-5_12

Lensink, M. F., Moal, I. H., Bates, P. A., Kastritis, P. L., Melquiond, A. S. J., Karaca, E., Schmitz, C., van Dijk, M., Bonvin, A. M. J. J., Eisenstein, M., Jimenez-Garcia, B., Grosdidier, S., Solernou, A., Perez-Cano, L., Pallara, C., Fernandez-Recio, J., Xu, J., Muthu, P., Kilambi, K. P., ... Wodak, S. J. (2014). Blind prediction of interfacial water positions in CAPRI. Proteins: Structure function and bioinformatics, 82(4), 620-632. https://doi.org/10.1002/prot.24439

Snijder, J., Burnley, R. J., Wiegard, A., Melquiond, A. S. J., Bonvin, A. M. J. J., Axmann, I. M., & Heck, A. J. R. (2014). Insight into cyanobacterial circadian timing from structural details of the KaiB-KaiC interaction. Proceedings of the National Academy of Sciences of the United States of America, 111(4), 1379-84. https://doi.org/10.1073/pnas.1314326111

2013

Scholarly publications

Janin, J., & Bonvin, A. M. J. J. (2013). Protein-protein interactions. Current Opinion in Structural Biology, 23(6), 859-861. https://doi.org/10.1016/j.sbi.2013.10.003

Bonvin, A. (2013). Coming to peace with protein complexes? 5th CAPRI evaluation meeting, April 17-19th 2013-Utrecht. Proteins: Structure, Function and Genetics, 81(12), 2073-2074. https://doi.org/10.1002/prot.24431

Alex, S., Lange, K., Amolo, T., Grinstead, J. S., Haakonsson, A. K., Szalowska, E., Koppen, A., Mudde, K., Haenen, D., Al-Lahham, S., Roelofsen, H., Houtman, R., van der Burg, B., Mandrup, S., Bonvin, A. M. J. J., Kalkhoven, E., Muller, M., Hooiveld, G. J., & Kersten, S. (2013). Short-Chain Fatty Acids Stimulate Angiopoietin-Like 4 Synthesis in Human Colon Adenocarcinoma Cells by Activating Peroxisome Proliferator-Activated Receptor gamma. Molecular and Cellular Biology, 33(7), 1303-1316. https://doi.org/10.1128/MCB.00858-12

Dias, D. M., Rodrigues, J. P. G. L. M., Domingues, N. S., Bonvin, A. M. J. J., & Castro, M. M. C. A. (2013). Unveiling the interaction of vanadium compounds with human serum albumin by using ¹H STD NMR and computational docking studies. European Journal of Inorganic Chemistry, 2013(26), 4619-4627. https://doi.org/10.1002/ejic.201300419

Moretti, R., Fleishman, S. J., Agius, R., Torchala, M., Bates, P. A., Kastritis, P. L., Garcia Lopes Maia Rodrigues, J., Trellet, M., Bonvin, A. M. J. J., Cui, M., Rooman, M., Gillis, D., Dehouck, Y., Moal, I., Romero-Durana, M., Perez-Cano, L., Pallara, C., Jimenez, B., Fernandez-Recio, J., ... Garcia Lopes Maia Rodrigues, J. (2013). Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins: Structure function and bioinformatics, 81(11), 1980-1987. https://doi.org/10.1002/prot.24356

van Dijk, M., Visscher, K. M., Kastritis, P., & Bonvin, A. M. J. J. (2013). Solvated protein–DNA docking using HADDOCK. Journal of Biomolecular NMR, 56, 51-63. https://doi.org/10.1007/s10858-013-9734-x
https://dspace.library.uu.nl/bitstream/handle/1874/290382/article_post-print.pdf?sequence=3

Bonvin, A. M. J. J., van Dijk, M., Karaca, E., Kastritis, P., Melquiond, A. S. J., Schmitz, C., & de Vries, S. J. (2013). Haddock. In G. C. K. Roberts (Ed.), Encyclopedia of Biophysics (pp. 943-945). Springer. https://doi.org/10.1007/978-3-642-16712-6_330

Alex, S., Lange, K., Amolo, T., Grinstead, J. S., Haakonsson, A. K., Szalowska, E., Koppen, A., Mudde, K., Haenen, D., Al-Lahham, S., Roelofsen, H., Houtman, R., van der Burg, B., Mandrup, S., Bonvin, A. M. J. J., Kalkhoven, E., Müller, M., Hooiveld, G. J., & Kersten, S. (2013). Short-chain fatty acids stimulate angiopoietin-like 4 synthesis in human colon adenocarcinoma cells by activating peroxisome proliferator-activated receptor γ. Molecular and Cellular Biology, 33(7), 1303-1316. https://doi.org/10.1128/MCB.00858-12

van der Schot, G., Zhang, Z., Vernon, R., Shen, Y., Vranken, W. F., Baker, D., Bonvin, A. M. J. J., & Lange, O. F. (2013). Improving 3D structure prediction from chemical shift data. Journal of Biomolecular NMR, 57, 27-35. https://doi.org/10.1007/s10858-013-9762-6

Karaca, E., & Bonvin, A. M. J. J. (2013). Advances in integrative modeling of biomolecular complexes. Methods, 59(3), 372-381. https://doi.org/10.1016/j.ymeth.2012.12.004

Karaca, E., & Bonvin, A. M. J. J. (2013). On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys. Acta crystallographica. Section D, biological crystallography, 69, 683-694. https://doi.org/10.1107/S0907444913007063

van der Cruijsen, E. A. W., Nand, D., Weingarth, M. H., Prokofyev, A., Hornig, S., Cukkemane, A. A., Bonvin, A. M. J. J., Becker, S., Hulse, R. E., Perozo, E., Pongs, O., & Baldus, M. (2013). The importance of the lipid-pore loop interface for potassium channel structure and function. Proceedings of the National Academy of Sciences of the United States of America, 110, 13008-13013. https://doi.org/10.1073/pnas.1305563110
https://dspace.library.uu.nl/bitstream/handle/1874/290404/1305563110.full.pdf?sequence=1

Weingarth, M. H., Prokofyev, A., van der Cruijsen, E. A. W., Nand, D., Bonvin, A. M. J. J., Pongs, O., & Baldus, M. (2013). Structural Determinants of Specific Lipid Binding to Potassium Channels. Journal of the American Chemical Society, 135(10), 3983-3988. https://doi.org/10.1021/ja3119114

Kastritis, P., & Bonvin, A. M. J. J. (2013). On the binding affinity of macromolecular interactions: daring to ask why proteins interact. Journal of the Royal Society Interface, 10(79), 1-28. [20120835]. https://doi.org/10.1098/rsif.2012.0835

Trellet, M., Melquiond, A. S. J., & Bonvin, A. M. J. J. (2013). A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking. PLoS One, 8(3), 1-13. [e58769]. https://doi.org/10.1371/journal.pone.0058769

Dagil, R., O'Shea, C., Nykjaer, A., Bonvin, A. M. J. J., & Kragelund, B. B. (2013). Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats: insight from the nmr structure of the 10th complement type repeat domain alone and in complex with gentamicin. Journal of Biological Chemistry, 288, 4424-4435. [288]. https://doi.org/10.1074/jbc.M112.434159

Janin, J., & Bonvin, A. M. J. J. (2013). Protein–protein interactions. Current Opinion in Structural Biology, 23, 859-861. https://doi.org/10.1016/j.sbi.2013.10.003

Varney, K. M., Bonvin, A. M. J. J., Pazgier, M., Malin, J., Yu, W., Ateh, E., Oashi, T., Lu, W., Huang, J., Diepeveen-de Buin, M., Bryant, J., Breukink, E. J., MacKerell, A. D., & de Leeuw, E. P. H. (2013). Turning Defense into Offense: Development of Defensin Mimetics as Novel Antibiotics targeting Lipid II. PLoS Pathogens, 9(11), [e1003732]. https://doi.org/10.1371/journal.ppat.1003732

Garcia Lopes Maia Rodrigues, J., Melquiond, A. S. J., Karaca, E., Trellet, M., van Dijk, M., van Zundert, G. C. P., Schmitz, C., de Vries, S. J., Bordogna, A., Bonati, L., Kastritis, P. L., Bonvin, A. M. J. J., & Garcia Lopes Maia Rodrigues, J. (2013). Defining the limits of homology modeling in information-driven protein docking. Proteins: Structure function and bioinformatics, 81(12), 2119-2128. https://doi.org/10.1002/prot.24382

Hulsik, D. L., Liu, Y. Y., Strokappe, N. M., Battella, S., el Khattabi, M., Bonvin, A. M. J. J., Verrips, C. T., & Rutten, L. (2013). A gp41 MPER-specific Llama VHH Requires a Hydrophobic CDR3 for Neutralization but not for Antigen Recognition. PLoS Pathogens, 9(3), 1-16. [e1003202]. https://doi.org/10.1371/journal.ppat.1003202

Bonvin, A. M. J. J. (2013). Coming to peace with protein complexes? 5th CAPRI evaluation meeting, April 17–19th 2013 – Utrecht. Proteins: Structure function and bioinformatics, 81(12), 2073-2074. https://doi.org/10.1002/prot.24431

Kastritis, P., Visscher, K. M., van Dijk, A. D. J., & Bonvin, A. M. J. J. (2013). Solvated protein-protein docking using Kyte-Doolittle-based water preferences. Proteins: Structure function and bioinformatics, 81(3), 510-518. https://doi.org/10.1002/prot.24210

2012

Scholarly publications

Weingarth, M., Nand, D., van der Cruijsen, E., Melquiond, A., Ader, C., Pongs, O., Becker, S., Bonvin, A. M. J. J., & Baldus, M. (2012). Unravelling supramolecular organisation of membrane proteins by solid state NMR and Molecular Dynamics simulations. FEBS Journal, 279, 256-256.

Markley, J. L., Akutsu, H., Asakura, T., Baldus, M., Boelens, R., Bonvin, A., Kaptein, R., Bax, A., Bezsonova, I., Gryk, M. R., Hoch, J. C., Korzhnev, D. M., Maciejewski, M. W., Case, D., Chazin, W. J., Cross, T. A., Dames, S., Kessler, H., Lange, O., ... Yokoyama, S. (2012). In support of the BMRB. Nature Structural and Molecular Biology, 19(9), 854-860. https://doi.org/10.1038/nsmb.2371

Hennig, J., de Vries, S., Hennig, K. D. M., Randles, L., Walters, K. J., Sunnerhagen, M., & Bonvin, A. MJJ. (2012). MTMDAT-HADDOCK: High-throughput, protein complex structure modeling based on limited proteolysis and mass spectrometry. BMC Structural Biology, 29. https://doi.org/10.1186/1472-6807-12-29

Gradmann, S. H. E., Ader, C., Heinrich, I., Nand, D., Dittmann, M., Cukkemane, A. A., van Dijk, M., Bonvin, A. M. J. J., Engelhard, M., & Baldus, M. (2012). Rapid prediction of multi-dimensional NMR data sets. Journal of Biomolecular NMR, 54(4), 377-387. https://doi.org/10.1007/s10858-012-9681-y

Kastritis, P., van Dijk, A. D. J., & Bonvin, A. M. J. J. (2012). Explicit Treatment of Water Molecules in Data-Driven Protein–Protein Docking: The Solvated HADDOCKing Approach. Methods in Molecular Biology, 819, 355-374. https://doi.org/10.1007/978-1-61779-465-0_22
https://dspace.library.uu.nl/bitstream/handle/1874/262520/Solvated_docking-post-print.pdf?sequence=3

Melquiond, A. S. J., Karaca, E., Kastritis, P., & Bonvin, A. M. J. J. (2012). Next challenges in protein–protein docking: from proteome to interactome and beyond. Wiley Interdisciplinary Reviews: Computational Molecular Science, 2(4), 642-651. https://doi.org/10.1002/wcms.91
https://dspace.library.uu.nl/bitstream/handle/1874/255698/WIREs_CMS_pre-peerreview%255B1%255D.pdf?sequence=3

van Dijk, M., Wassenaar, T. A., & Bonvin, A. M. J. J. (2012). A flexible, grid-enabled web portal for GROMACS molecular dynamics simulations. Journal of Chemical Theory and Computation, 8(10), 3463-3472. https://doi.org/10.1021/ct300102d

Garcia Lopes Maia Rodrigues, J., Trellet, M., Schmitz, C., Kastritis, P., Karaca, E., Melquiond, A. S. J., Bonvin, A. M. J. J., & Garcia Lopes Maia Rodrigues, J. (2012). Clustering biomolecular complexes by residue contacts similarity. Proteins: Structure function and bioinformatics, 80(7), 1810-1817. https://doi.org/10.1002/prot.24078

Kastritis, P., & Bonvin, A. M. J. J. (2012). Predicting and Dissecting High-order Molecular Complexity by Information-driven Biomolecular Docking. In G. Tegos, & E. Mylonakis (Eds.), Antimicrobial drug discovery: emerging strategies (pp. 232-246). (Advances in molecular and cellular microbiology; No. 22). CABI. https://doi.org/10.1079/9781845939434.0338

Schmitz, C., Melquiond, A. S. J., de Vries, S. J., Karaca, E., van Dijk, M., Kastritis, P., & Bonvin, A. M. J. J. (2012). Protein–Protein Docking with HADDOCK. In I. Bertini, K. S. McGreevy, & G. Parigi (Eds.), NMR of biomolecules : towards mechanistic systems biology (pp. 520-535). Wiley. https://doi.org/10.1002/9783527644506.ch32

Wassenaar, T. A., de Vries, S. J., Bonvin, A. M. J. J., & Bekker, H. (2012). SQUEEZE-E: The optimal solution for molecular simulations with periodic boundary conditions. Journal of Chemical Theory and Computation, 8(10), 3618-3627. https://doi.org/10.1021/ct3000662

van Wijk, S. J. L., Melquiond, A. S. J., de Vries, S. J., Timmers, H. T. M., & Bonvin, A. M. J. J. (2012). Dynamic control of selectivity in the ubiquitination pathway revealed by an ASP to GLU substitution in an intra-molecular salt-bridge network. PLoS Computational Biology, 8(11), e1002754. [e1002754]. https://doi.org/10.1371/journal.pcbi.1002754

2011

Scholarly publications

Neumoin, A., Leonchiks, A., Petit, P., Vuillard, L., Pizza, M., Soriani, M., Boelens, R., & Bonvin, A. M. J. J. (2011). H-1, C-13 and N-15 assignment of the GNA1946 outer membrane lipoprotein from Neisseria meningitidis. Biomolecular NMR Assignments, 5(2), 135-138. https://doi.org/10.1007/s12104-010-9285-y

Wu, A. M., Singh, T., Liu, J-H., André, S., Lensch, M., Siebert, H-C., Krzeminski, M. N., Bonvin, A. M. J. J., Kaltner, H., & Wu, J. H. (2011). Adhesion/growth-regulatory galectins: insights into their ligand selectivity using natural glycoproteins and glycotopes. In The Molecular Immunology of Complex Carbohydrates-3 (3 ed., Vol. 705, pp. 117-141). (Advances in Experimental Medicine and Biology). Springer. https://doi.org/10.1007/978-1-4419-7877-6_7

Kastritis, P. L., & Bonvin, A. M. J. J. (2011). Erratum: Are scoring functions in protein - Protein Docking Ready to predict interactomes? Clues from a novel binding affinity benchmark (Journal of Proteome Research (2010) 9 (2216-2225). Journal of Proteome Research, 10(2), 921-922. https://doi.org/10.1021/pr101118t

Koehler, C., Carlier, L. P. A., Veggi, D., Balducci, E., Di Marcello, F., Ferrer-Navarro, M., Pizza, M., Daura, X., Soriani, M., Boelens, R., & Bonvin, A. M. J. J. (2011). Structural and biochemical characterization of NarE, an iron-containing ADP-ribosyltransferase from Neisseria meningitidis. Journal of Biological Chemistry, 286(17), 14842-14851. https://doi.org/10.1074/jbc.M110.193623

Krzeminski, M. N., Singh, T., André, S., Lensch, M., Wu, A. M., Bonvin, A. M. J. J., & Gabius, H-J. (2011). Human galectin-3 (Mac-2 antigen): Defining molecular switches of affinity to natural glycoproteins, structural and dynamic aspects of glycan binding by flexible ligand docking and putative regulatory sequences in the proximal promoter region. Biochimica et Biophysica Acta-General Subjects, 1810(2), 150-161. https://doi.org/10.1016/j.bbagen.2010.11.001

Neumoin, A., Leonchiks, A., Petit, P., Vuillard, L., Pizza, M., Soriani, M., Boelens, R., & Bonvin, A. M. J. J. (2011). 1H, 13C and 15N assignment of the GNA1946 outer membrane lipoprotein from Neisseria meningitidis. Biomolecular NMR Assignments, 5(2), 135-138. https://doi.org/10.1007/s12104-010-9285-y

Stratmann, D. P., Boelens, R., & Bonvin, A. M. J. J. (2011). Quantitative use of chemical shifts for the modeling of protein complexes. Proteins: Structure function and bioinformatics, 79(9), 2662-2670. https://doi.org/10.1002/prot.23090
https://dspace.library.uu.nl/bitstream/handle/1874/213115/Proteins-revised1.pdf?sequence=3

Escobar-Cabrera, E., Okon, M., Lau, D. K. W., Dart, C. F., Bonvin, A. M. J. J., & McIntosh, L. P. (2011). Characterizing the N- and C-terminal Small Ubiquitin-like Modifier (SUMO)-interacting Motifs of the Scaffold Protein DAXX. Journal of Biological Chemistry, 286(22), 19816-19829. https://doi.org/10.1074/jbc.M111.231647

Fleishman, S. J., Kastritis, P., & Bonvin, A. M. J. J. (2011). Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology, 414(2), 289-302. https://doi.org/10.1016/j.jmb.2011.09.031

de Vries, S. J., & Bonvin, A. M. J. J. (2011). CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK. PLoS One, 6(3), e17695/1-e17695/12. https://doi.org/10.1371/journal.pone.0017695

Carlier, L. P. A., Köhler, C., Veggi, D., Pizza, M., Soriani, M., Boelens, R., & Bonvin, A. M. J. J. (2011). NMR resonance assignments of NarE, a putative ADP-ribosylating toxin from Neisseria meningitidis. Biomolecular NMR Assignments, 5(1), 35-38. https://doi.org/10.1007/s12104-010-9261-6

Kastritis, P., Moal, I. H., Hwang, H., Weng, Z., Bates, P. A., Bonvin, A. M. J. J., & Janin, J. (2011). A structure-based benchmark for protein–protein binding affinity. Protein Science, 20(3), 482-491. https://doi.org/10.1002/pro.580

Schmitz, C. P. F., & Bonvin, A. M. J. J. (2011). Protein–protein HADDocking using exclusively pseudocontact shifts. Journal of Biomolecular NMR, 50, 263-266. https://doi.org/10.1007/s10858-011-9514-4

Fiamegos, Y. C., Kastritis, P., Exarchou, V., Han, H., Bonvin, A. M. J. J., Vervoort, J., Lewis, K., Hamblin, M. R., & Tegos, G. P. (2011). Antimicrobial and efflux pump inhibitory activity of caffeoylquinic acids from Artemisia absinthium against Gram-positive pathogenic bacteria. PLoS One, 6(4), e18127/1-e18127/12. https://doi.org/10.1371/journal.pone.0018127

2010

Scholarly publications

Melquiond, A. S. J., & Bonvin, A. M. J. J. (2010). Data-driven docking: Using external information to spark the biomolecular rendez-vous. In M. Zacharias (Ed.), Protein-Protein Complexes: Analysis, Modeling and Drug Design (pp. 182-208). Imperial College Press. https://doi.org/10.1142/9781848163409_0007

Bonvin, A. M. J. J., Rosato, A., & Wassenaar, T. A. (2010). The eNMR platform for structural biology. Journal of Structural and Functional Genomics, 11(1), 1-8. https://doi.org/10.1007/s10969-010-9084-9

de Vries, S. J., van Dijk, M., & Bonvin, A. M. J. J. (2010). The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, 5(5), 883-897. https://doi.org/10.1038/nprot.2010.32

Ferreira, N. L., Wassenaar, T. A., de Vries, S. J., van Dijk, M., van der Schot, G., van der Zwan, J., Boelens, R., Bonvin, A. M. J. J., Giachetti, A., Carotenuto, D., Rosato, A., Bertini, I., Herrmann, T., Bagaria, A., Zharavin, V., Jonker, H. R. A., Güntert, P., Schwalbe, H., & Vranken, W. F. (2010). e-NMR gLite grid enabled infrastructure. In A. Proença, A. Pina, J. García Tobío, & L. Ribeiro (Eds.), Ibergrid 2010 : 4th Iberian Grid Infrastructure Conference (May 2010, Braga, Portugal) (pp. 360-380). (Computacion). Netbiblo.

de Vries, S. J., Melquiond, A. S. J., Kastritis, P., Karaca, E., Bordogna, A., van Dijk, M., Rodrigues, J. P. G. L. M., & Bonvin, A. M. J. J. (2010). Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions. Proteins: Structure function and bioinformatics, 78(15), 3242-3249. https://doi.org/10.1002/prot.22814

Krzeminski, M., Loth, K., Boelens, R., & Bonvin, A. M. J. J. (2010). SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes. BMC Bioinformatics, 11(51), 1-8. https://doi.org/10.1186/1471-2105-11-51
https://dspace.library.uu.nl/bitstream/handle/1874/202696/SAMPLEX_2010_BMC-Bioinformatics.pdf?sequence=1

Nicastro, G., Todi, S. V., Karaca, E., Bonvin, A. M. J. J., Paulson, H. L., & Pastore, A. (2010). Understanding the role of the Josephin domain in the polyUb binding and cleavage properties of ataxin-3. PLoS One, 5(8), e12430/1-e12430/10. https://doi.org/10.1371/journal.pone.0012430
https://dspace.library.uu.nl/bitstream/handle/1874/202591/Understanding-the-role-of-the-josephin-domain_2010_PLoS-ONE.pdf?sequence=1

van Dijk, M., & Bonvin, A. M. J. J. (2010). Pushing the limits of what is achievable in protein-DNA docking: Benchmarking HADDOCK's performance. Nucleic Acids Research, 38(17), 5634-5647. https://doi.org/10.1093/nar/gkq222

Kobayashi, M., AB, E., Bonvin, A. M. J. J., & Siegal, G. (2010). Structure of the DNA-bound BRCA1 C-terminal region from human replication factor C p140 and model of the protein-DNA complex. Journal of Biological Chemistry, 285(13), 10087-10097. https://doi.org/10.1074/jbc.M109.054106

2009

Scholarly publications

van Wijk, S. J. L., de Vries, S. J., Kemmeren, P., Huang, A., Boelens, R., Bonvin, A. M. J. J., & Timmers, H. T. M. (2009). A comprehensive framework of E2–RING E3 interactions of the human ubiquitin–proteasome system. Molecular Systems Biology, 5(1), 1-1. https://doi.org/10.1038/msb.2009.76

Krzeminski, M., Fuentes, G., Boelens, R., & Bonvin, A. M. J. J. (2009). Minoes: A new approach to select a representative ensemble of structures in NMR studies of [partially] unfolded states. Application to Delta 25-PYP. Proteins: Structure, Function and Genetics, 74(4), 895-904. https://doi.org/10.1002/prot.22197

Van Wijk, S. J. L., De Vries, S. J., Kemmeren, P., Huang, A., Boelens, R., Bonvin, A. M. J. J., & Timmers, H. T. M. (2009). Erratum: A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system (Molecular Systems Biology (2009) 5 (295) DOI: 10.1038/msb.2009.55). Molecular Systems Biology [E], 5, [317]. https://doi.org/10.1038/msb.2009.76

Eggink, D., Langedijk, J. P. M., Bonvin, A. M. J. J., Deng, Y., Lu, M., Berkhout, B., & Sanders, R. W. (2009). Detailed mechanistic insights into HIV-1 sensitivity to three generations of fusion inhibitors. Journal of Biological Chemistry, 284(39), 26941-26950. https://doi.org/10.1074/jbc.M109.004416

van Dijk, M., & Bonvin, A. M. J. J. (2009). 3D-DART: a DNA structure modelling server. Nucleic Acids Research, 37(Suppl. 2), W235-W239. https://doi.org/10.1093/nar/gkp287

Jung, S., Dingley, A. J., Augustin, R., Anton-Erxleben, F., Stanisak, M., Gelhaus, C., Gutsmann, T., Hammer, M. U., Podschun, R., Bonvin, A. M. J. J., Leippe, M., Bosch, T. C. G., & Grötzinger, J. (2009). Hydramacin-1, structure and antibacterial activity of a protein from the basal metazoan hydra. Journal of Biological Chemistry, 284(3), 1896-1905. https://doi.org/10.1074/jbc.M804713200

van Wijk, S. J. L., de Vries, S. J., Kemmeren, P. P. C. W., Huang, A., Boelens, R., Bonvin, A. M. J. J., & Timmers, H. T. M. (2009). A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system. Molecular Systems Biology [E], 5, 295. https://doi.org/10.1038/msb.2009.55

Romanuka, J., Folkers, G. E., Biris, N., Tishchenko, E., Wienk, H. L. J., Bonvin, A. M. J. J., Kaptein, R., & Boelens, R. (2009). Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein–DNA complexes. Journal of Molecular Biology, 390(3), 478-489. https://doi.org/10.1016/j.jmb.2009.05.022

Rutten, L., Mannie, J-PBA., Stead, C. M., Raetz, C. R. H., Reynolds, C. M., Bonvin, A. M. J. J., Tommassen, J. P. M., Egmond, M. R., Trent, M. S., & Gros, P. (2009). Active-site architecture and catalytic mechanism of the lipid A deacylase LpxR of Salmonella typhimurium. Proceedings of the National Academy of Sciences of the United States of America, 106(6), 1960-1964. https://doi.org/10.1073/pnas.0813064106
https://dspace.library.uu.nl/bitstream/handle/1874/42725/1960.full.pdf?sequence=1

Stockner, T., de Vries, S. J., Bonvin, A. M. J. J., Ecker, G. F., & Chiba, P. (2009). Data-driven homology modelling of P-glycoprotein in the ATP-bound state indicates flexibility of the transmembrane domains. The FEBS journal, 276(4), 964-972. https://doi.org/10.1111/j.1742-4658.2008.06832.x
https://dspace.library.uu.nl/bitstream/handle/1874/42867/fulltext.pdf?sequence=1

Rosato, A., van der Schot, G., & Bonvin, A. M. J. J. (2009). CASD-NMR: critical assessment of automated structure determination by NMR. Nature Methods, 6(9), 625-626. https://doi.org/10.1038/nmeth0909-625.

2008

Scholarly publications

Correa, F., Salinas, R. K., Bonvin, A. M. J. J., & Farah, C. S. (2008). Deciphering the role of the electrostatic interactions in the alpha-tropomyosin head-to-tail complex. Proteins: Structure, Function and Genetics, 73(4), 902-917. https://doi.org/10.1002/prot.22116

De Vries, S. J., Van Dijk, M., & Bonvin, A. M. J. J. (2008). The Prediction of Macromolecular Complexes by Docking. In J. M. Bujnicki (Ed.), Prediction of Protein Structures, Functions, and Interactions (pp. 211-230). Wiley. https://doi.org/10.1002/9780470741894.ch9

Fuentes, G., van Dijk, A. D. J., & Bonvin, A. M. J. J. (2008). Nuclear Magnetic Resonance-based modeling and refinement of protein three-dimensional structures and their complexes. In A. Kukol (Ed.), Molecular modeling of proteins (pp. 229-255). (Methods in molecular biology; No. 443). Humana Press. https://doi.org/10.1007/978-1-59745-177-2_13

Correa, F., Kopke Salinas, R., Bonvin, A. M. J. J., & Farah, C. S. (2008). Deciphering the role of the electrostatic interactions in the α-tropomyosin head-to-tail complex. Proteins: Structure function and bioinformatics, 73(4), 902-917. https://doi.org/10.1002/prot.22116, https://doi.org/2552749

Arnusch, C. J., Bonvin, A. M. J. J., Verel, A. M., Jansen, W. T. M., Liskamp, R. M. J., de Kruijff, B., Pieters, R. J., & Breukink, E. J. (2008). The vancomycin-nisin(1-12) hybrid restores activity against vancomycin resistant enterococci. Biochemistry, 47(48), 12661-12663. https://doi.org/10.1021/bi801597b

Sanders, R. W., Hsu, S. T., van Anken, E., Liscaljet, I. M., Dankers, M., Bontjer, I., Land, A., Braakman, L. J., Bonvin, A. M. J. J., & Berkhout, B. (2008). Evolution rescues folding of Human Immunodeficiency Virus-1 envelope glycoprotein GP120 lacking a conserved disulfide bond. Molecular Biology of the Cell, 19(11), 4707-4716. https://doi.org/10.1091/mbc.e08-07-0670

Krzeminski, M. N., Fuentes, G., Boelens, R., & Bonvin, A. M. J. J. (2008). MINOES: a new approach to select a representative ensemble of structures in NMR studies of (partially) unfolded states : application to Δ25-PYP. Proteins: Structure function and bioinformatics, 74(4), 895-904. https://doi.org/10.1002/prot.22197
https://dspace.library.uu.nl/bitstream/handle/1874/33301/547.pdf?sequence=1

van Dijk, M., & Bonvin, A. M. J. J. (2008). A protein–DNA docking benchmark. Nucleic Acids Research, 36(14), e88/1-e88/5. https://doi.org/10.1093/nar/gkn386
https://dspace.library.uu.nl/bitstream/handle/1874/33227/548.pdf?sequence=1

Repanas, K., Fuentes, G., Cohen, S., Bonvin, A. M. J. J., & Perrakis, A. (2008). Insights into the DNA cleavage mechanism of human LINE-1 retrotransposon endonuclease. Proteins: Structure function and bioinformatics, 74(4), 917-927. https://doi.org/10.1002/prot.22201

2007

Scholarly publications

De Vries, S. J., van Dijk, A. D. J., Krzeminski, M., van Dijk, M., Thureau, A., Hsu, V., Wassenaar, T., & Bonvin, A. M. J. J. (2007). HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets. Proteins: Structure, Function and Genetics, 69(4), 726-733. https://doi.org/10.1002/prot.21723

Tomaselli, S., Ragona, L., Zetta, L., Assfalg, M., Ferranti, P., Longhi, R., Bonvin, A. M. J. J., & Molinari, H. (2007). NMR-based modeling and binding studies of a ternary complex between chicken liver bile acid binding protein and bile acids. Proteins: Structure, Function and Genetics, 69(1), 177-191. https://doi.org/10.1002/prot.21517

Jeninga, E. H., van Beekum, O., van Dijk, A. D. J., Hamers, N., Hendriks-Stegeman, B. I., Bonvin, A. M. J. J., Berger, R., & Kalkhoven, E. (2007). Impaired peroxisome proliferator-activated receptor gamma function through mutation of a conserved salt bridge (R425C) in familial partial lipodystrophy. Molecular Endocrinology, 21(5), 1049-1065. https://doi.org/10.1210/me.2006-0485

Correa, F., Salinas, R. K., Bonvin, A., & Farah, C. S. (2007). Structure and stability analysis of the skeletal alpha-tropomyosin head-to-tail complex. Biophysical Journal, 626A-627A.

van Dijk, A. D. J., Ciofi-Baffoni, S., Banci, L., Bertini, I., Boelens, R., & Bonvin, A. M. J. J. (2007). Modeling protein-protein complexes involved in the cytochrome c oxidase copper-delivery pathway. Journal of Proteome Research, 6(4), 1530-1539. https://doi.org/10.1021/pr060651f

Bonvin, A. M. J. J., Boelens, R., & Kaptein, R. (2007). Protein Structures: Relaxation Matrix Refinement. eMagRes, 2007. https://doi.org/10.1002/9780470034590.emrstm0423

Gelis, I., Bonvin, A. M. J. J., Keramisanou, D., Koukaki, M., Gouridis, G., Karamanou, S., Economou, A., & Kalodimos, C. G. (2007). Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Determined by NMR. Cell, 131(4), 756-769. https://doi.org/10.1016/j.cell.2007.09.039

van Dijk, A. D. J., Ciofi-Baffoni, S., Banci, L., Bertini, I., Boelens, R., & Bonvin, A. M. J. J. (2007). Modelling protein-protein complexes involved in the cytochrome c oxidase copper-delivery pathway. Journal of Proteome Research, 6(4), 1530-1539. https://doi.org/10.1021/pr060651f

Wu, A. M., Singh, T., Liu, J-H., Krzeminski, M. N., Russwurm, R., Siebert, H-C., Bonvin, A. M. J. J., André, S., & Gabius, H-J. (2007). Activity-structure correlations in divergent lectin-evolution: fine specificity of chicken galectin CG-14 and computational analysis of flexible ligand docking for CG-14 and the closely related CG-16. Glycobiology, 17, 165-184. https://doi.org//10.1093/glycob/cwl062, https://doi.org/Activity-structure correlations in divergent lectin-evolution: fine specificity of chicken galectin CG-14 and computational analysis of flexible ligand docking for CG-14 and the closely related CG-16

Tomasell, S., Ragona, L., Zetta, L., Assfalg, M., Ferranti, P., Longhi, R., Bonvin, A. M. J. J., & Molinari, H. (2007). NMR-based modelling and binding studies of a ternary complex between chicken liver bile acid binding protein and bile acids. Proteins: Structure function and bioinformatics, 69, 177-191. https://doi.org/10.1002/prot.21517

Jeninga, E. H., van Beekum, P. O., van Dijk, A. D. J., Hamers, N., Bonvin, A. M. J. J., Berger, R., & Kalkhoven, E. (2007). Impaired peroxisome proliferator-activated receptor γ function through mutation of a conserved salt bridge (R425C) in familial partial lipodystrophy. Journal of Molecular Endocrinology, 21(5), 1049-1065. https://doi.org/10.1210/me.2006-0485

de Vries, S. J., van Dijk, A. D. J., Krzeminski, M. N., van Dijk, M., Thureau, A. J. M. M., Hsu, V., Wassenaar, T. A., & Bonvin, A. M. J. J. (2007). HADDOCK versus HADDOCK: New features and performance of HADDOCK 2.0 on the CAPRI targets. Proteins: Structure function and bioinformatics, 69(4), 726-733. https://doi.org/10.1002/prot.21723, https://doi.org/10.1002/prot.21723

2006

Scholarly publications

Langedijk, J. P. M., Fuentes, G., Boshuizen, R., & Bonvin, A. M. J. J. (2006). Two-rung model of a left-handed beta-helix for prions explains species barrier and strain variation in transmissible spongiform encephalopathies. Journal of Molecular Biology, 360(4), 907-920. https://doi.org/10.1016/j.jmb.2006.05.042

Fuchs, PFJ., Bonvin, AMJJ., Bochicchio, B., Pepe, A., Alix, AJP., & Tamburro, AM. (2006). Kinetics and thermodynamics of type VIII beta-turn formation: A CD, NMR, and microsecond explicit molecular dynamics study of the GDNP tetrapeptide. Biophysical Journal, 90(8), 2745-2759. https://doi.org/10.1529/biophysj.105.074401

Tomaselli, S., Esposito, V., Vangone, P., van Nuland, NAJ., Bonvin, AMJJ., Guerrini, R., Tancredi, T., Temussi, PA., & Picone, D. (2006). The alpha-to-beta conformational transition of Alzheimer's A beta-(1-42) peptide in aqueous media is reversible: A step by step conformational analysis suggests the location of beta conformation seeding. ChemBioChem, 7(2), 257-267. https://doi.org/10.1002/cbic.200500223

Volkov, A. N., Ferrari, D., Worrall, J. A. R., Bonvin, A. M. J. J., & Ubbink, M. (2006). Erratum: The orientations of cytochrome c in the highly dynamic complex with cytochrome b5visualized by NMR and docking using HADDOCK (Protein Science (2005) 14 (799-811)). Protein Science, 15(6), 1563.
https://dspace.library.uu.nl/bitstream/handle/1874/385158/Erratum_The_orientations_of_cytochrome_c_in_the_highly_dynamic_complex_with_cytochrome_b5visualized_by_NMR_and_docking_using_HADDOCK_Protein_Science_2005_14_799_811_.pdf?sequence=1

AB, E., Pugh, D. J. R., Kaptein, R., Boelens, R., & Bonvin, A. M. J. J. (2006). Direct Use of Unassigned Resonances in NMR Structure Calculations with Proxy Residues. Journal of the American Chemical Society, 128(23), 7566-7571. https://doi.org/10.1021/ja058504q

van Dijk, A. D. J., Kaptein, R., Boelens, R., & Bonvin, A. M. J. J. (2006). Combining NMR relaxation with chemical shift perturbation data to drive protein–protein docking. Journal of Biomolecular NMR, 34, 237-244. https://doi.org/10.1007/s10858-006-0024-8

Grinstead, J. S., Hsu, S. T., Laan, W., Bonvin, A. M. J. J., Hellingwerf, K. J., Boelens, R., & Kaptein, R. (2006). The Solution Structure of the AppA BLUF Domain: Insight into the Mechanism of Light-Induced Signaling. ChemBioChem, 7(1), 187-193. https://doi.org/10.1002/cbic.200500270

Tomaselli, S., Esposito, V., Vangone, P., van Nuland, N. A. J., Bonvin, A. M. J. J., Guerrini, R., Tancredi, T., Temussi, P. A., & Picone, D. (2006). The α-to-β Conformational Transition of Alzheimer’s Aβ-(1–42) Peptide in Aqueous Media is Reversible: A Step by Step Conformational Analysis Suggests the Location of β Conformation Seeding. ChemBioChem, 7, 257-267. https://doi.org/10.1002/cbic.200500223

Sibille, N., Favier, A., Azuaga, A. I., Ganshaw, G., Bott, R., Bonvin, A. M. J. J., Boelens, R., & van Nuland, N. A. J. (2006). Comparative NMR study on the impact of point mutations on protein stability of Pseudomonas mendocina lipase. Protein Science, 15(8), 1915-1927. https://doi.org/10.1110/ps.062213706

de Vries, S. J., & Bonvin, A. M. J. J. (2006). Intramolecular surface contacts contain information about protein–protein interface regions. Bioinformatics, 22(17), 2094-2098. https://doi.org/10.1093/bioinformatics/btl275

van Dijk, A. D. J., & Bonvin, A. M. J. J. (2006). Solvated docking: introducing water into the modelling of biomolecular complexes. Bioinformatics, 22(19), 2340-2347. https://doi.org/10.1093/bioinformatics/btl395

Fuchs, P. F. J., Bonvin, A. M. J. J., Bochicchio, B., Pepe, A., Alix, A. J. P., & Tamburro, A. M. (2006). Kinetics and Thermodynamics of Type VIII β-Turn Formation: A CD, NMR, and Microsecond Explicit Molecular Dynamics Study of the GDNP Tetrapeptide. Biophysical Journal, 90, 2745-2759. https://doi.org/10.1529/biophysj.105.074401

de Vries, S. J., van Dijk, A. D. J., & Bonvin, A. M. J. J. (2006). WHISCY: What Information Does Surface Conservation Yield? Application to Data-Driven Docking. Proteins: Structure function and bioinformatics, 63(3), 479-489. https://doi.org/10.1002/prot.20842

Kamphuis, M. B., Bonvin, A. M. J. J., Monti, M. C., Lemonnier, M., Munoz-Gomez, A., van den Heuvel, R. H. H., Diaz-Orejas, R., & Boelens, R. (2006). Model for RNA binding and the catalytic site of the RNase Kid of the bacterial parD toxin-antitoxin system. Journal of Molecular Biology, 357, 115-126.
https://dspace.library.uu.nl/bitstream/handle/1874/19818/38_model.pdf?sequence=1

Langedijk, J. P., Fuentes, G., Boshuizen, R., & Bonvin, A. M. J. J. (2006). Two-rung Model of a Left-handed β-Helix for Prions Explains Species Barrier and Strain Variation in Transmissible Spongiform Encephalopathies. Journal of Molecular Biology, 360, 907-920. https://doi.org/10.1016/j.jmb.2006.05.042

Rutten, L., Geurtsen, J. J. G., Lambert, W., Smolenaers, J. J. M., Bonvin, A. M., de Haan, A., van der Ley, P., Egmond, M. R., Gros, P., & Tommassen, J. P. M. (2006). Crystal structure and catalytic mechanism of the LPS 3-O-deacylase PagL from Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences of the United States of America, 103, 7071-7076. https://doi.org/10.1073/pnas.0509392103

Bonvin, A. M. J. J. (2006). Flexible protein–protein docking. Current Opinion in Structural Biology, 16, 194-200. https://doi.org/10.1016/j.sbi.2006.02.002

Jensen, G. A., Andersen, O. M., Bonvin, A. M. J. J., Bjerrum-Bohr, I., Etzerodt, M., Thøgersen, H. C., O'Shea, C., Poulsen, F. M., & Kragelund, B. B. (2006). Binding Site Structure of One LRP–RAP Complex: Implications for a Common Ligand–Receptor Motif Binding. Journal of Molecular Biology, 362, 700-716. https://doi.org/10.1016/j.jmb.2006.07.013

2005

Scholarly publications

Fuentes, G., Nederveen, AJ., Kaptein, R., Boelens, R., & Bonvin, AMJJ. (2005). Describing partially unfolded states of proteins from sparse NMR ddata. Journal of Biomolecular NMR, 33(3), 175-186. https://doi.org/10.1007/s10858-005-3207-9

Lin, KF., Liu, YN., Hsu, STD., Samuel, D., Cheng, CS., Bonvin, AMJJ., & Lyu, PC. (2005). Characterization and structural analyses of nonspecific lipid transfer protein 1 from Mung Bean (vol 44, pg 5703, 2005). Biochemistry, 44(34), 11646-11646. https://doi.org/10.1021/bi0580207

van Dijk, A-J., de Vries, SJ., Dominguez, C., Chen, H., Zhou, HX., & Bonvin, AMJJ. (2005). Data-driven docking: HADDOCK's adventures in CAPRI. Proteins: Structure, Function and Genetics, 60(2), 232-238. https://doi.org/10.1002/prot.20563

Doreleijers, JF., Nederveen, AJ., Vranken, W., Lin, JD., Bonvin, AMJJ., Kaptein, R., Markley, JL., & Ulrich, EL. (2005). BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. Journal of Biomolecular NMR, 32(1), 1-12. https://doi.org/10.1007/s10858-005-2195-0

Nederveen, AJ., & Bonvin, AMJJ. (2005). NMR relaxation and internal dynamics of ubiquitin from a 0.2 mu s MD simulation. Journal of Chemical Theory and Computation, 1(3), 363-374. https://doi.org/10.1021/ct0498829

Volkov, AN., Ferrari, D., Worrall, JAR., Bonvin, AMJJ., & Ubbink, M. (2005). The orientations of cytochrome c in the highly dynamic complex with cytochrome b(5) visualized by NMR and docking using HADDOCK. Protein science, 14(3), 799-811. https://doi.org/10.1110/ps.041150205

Hsu, STD., Peter, C., van Gunsteren, WF., & Bonvin, AMJJ. (2005). Entropy calculation of HIV-1 env gp120, its receptor CD4, and their complex: An analysis of configurational entropy changes upon complexation. Biophysical Journal, 88(1), 15-24. https://doi.org/10.1529/biophysj.104.044933

Tomaselli, S., van Nuland, NAJ., Bonvin, AMJJ., Salvadori, S., Tancredi, T., Temuss, PA., & Picone, D. (2005). Experimental evidence for a reversible alfa to beta transition of abeta-(1-42) in aqueous media: A step by step conformational analysis pinpoints the location of the beta conformation seedling. Biopolymers, 80(4), 595-595.

Lin, K. F., Liu, Y. N., Hsu, S. T. D., Samuel, D., Cheng, C. S., Bonvin, A. M. J. J., & Lyu, P. C. (2005). Erratum: Characterization and structural analyses of nonspecific lipid transfer protein 1 from Mung bean (Biochemistry (April 19, 2005) 44, 15 (5703-5712)). Biochemistry, 44(34), 11646. https://doi.org/10.1021/bi0580207

Lin, K-F., Liu, Y-N., Hsu, S-T. D., Samuel, D., Cheng, C-S., Bonvin, A. M. J. J., & Lyu, P-C. (2005). Characterization and structural analyses of nonspecific lipid transfer protein 1 from mung bean. Biochemistry, 44(15), 5703-5712. [15]. https://doi.org/10.1021/bi047608v

Salinas, R. K., Folkers, G. E., Bonvin, A. M. J. J., Das, D., Boelens, R., & Kaptein, R. (2005). Altered specificity in DNA binding by the lac repressor: A mutant lac headpiece that mimics the gal repressor. ChemBioChem, 6(9), 1628-1637. https://doi.org/10.1002/cbic.200500049

Van Dijk, A. D. J., Boelens, R., & Bonvin, A. M. J. J. (2005). Data-driven docking for the study of biomolecular complexes. The FEBS journal, 272(2), 293-312. https://doi.org/10.1111/j.1742-4658.2004.04473.x

Doreleijers, J. F., Nederveen, A. J., Vranken, W., Lin, J., Bonvin, A. M. J. J., Kaptein, R., Markley, J. L., & Ulrich, E. L. (2005). BioMagResBank databases DOCR and FRED with converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. Journal of Biomolecular NMR, 32, 1-12. https://doi.org/10.1007/s10858-005-2195-0

Nederveen, A. J., & Bonvin, A. M. J. J. (2005). NMR relaxation and internal dynamics of ubiquitin from a 0.2 μsecond MD simulation. Journal of Chemical Theory and Computation, 1, 345-352. https://doi.org/10.1021/ct0498829

Hsu, S. T., Peter, C., van Gunsteren, W. F., & Bonvin, A. M. J. J. (2005). Entropy calculation of HIV-1 Env gp120, its receptor CD4 and their complex: an analysis of entropy changes upon complexation. Biophysical Journal, 88, 15-24. https://doi.org/10.1529/biophysj.104.044933

Nederveen, A. J., Doreleijers, J. F., Vranken, W., Miller, Z., Spronk, C. A. E. M., Nabuurs, S. B., Guntert, P., Livny, M., Markley, J. L., Nilges, M., Ulrich, E. L., Kaptein, R., & Bonvin, A. M. J. J. (2005). RECOORD: a Recalculated COORdinates Database of 500+ proteins from PDB using restraints from the BioMagResBank. Proteins: Structure function and bioinformatics, 59, 662-672. https://doi.org/10.1002/prot.20408

Volkov, A. N., Ferrari, D., Worrall, J. A. R., Bonvin, A. M. J. J., & Ubbink, M. (2005). The orientations of cytochrome c in the highly dynamic complex with cytochrome b5 visualized by NMR and docking using HADDOCK. Protein Science, 14, 799-811. https://doi.org/10.1110/ps.041150205

Fuentes, G., Nederveen, A. J., Kaptein, R., Boelens, R., & Bonvin, A. M. J. J. (2005). Describing partially unfolded states of proteins from sparse NMR data. Journal of Biomolecular NMR, 33, 175-186. https://doi.org/10.1007/s10858-005-3207-9

van Dijk, A. D. J., de Vries, S. J., Dominguez, C., Chen, H., Zhou, H-X., & Bonvin, A. M. J. J. (2005). Data-driven docking: HADDOCK’s adventures in CAPRI. Proteins: Structure function and bioinformatics, 60, 232-238. https://doi.org/10.1002/prot.20563

van Dijk, A. D. J., Fushman, D., & Bonvin, A. M. J. J. (2005). Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data. Proteins: Structure function and bioinformatics, 60, 367-381. https://doi.org/10.1002/prot.20476

Bonvin, A. M. J. J., Boelens, R., & Kaptein, R. (2005). NMR analysis of protein interactions. Current Opinion in Chemical Biology, 9, 501-508. https://doi.org/10.1016/j.cbpa.2005.08.011

2004

Scholarly publications

Tzakos, A. G., Fuchs, P., Van Nuland, N. A. J., Troganis, A., Tselios, T., Deraos, S., Matsoukas, J., Gerothanassis, I. P., & Bonvin, A. M. J. J. (2004). NMR and molecular dynamics studies of an autoimmune myelin basic protein peptide and its antagonist: Structural implications for the MHC II (I-A u)-peptide complex from docking calculations. European Journal of Biochemistry, 271(16), 3399-3413. https://doi.org/10.1111/j.1432-1033.2004.04274.x

Hsu, S-T. D., Breukink, E., Tischenko, E., Lutters, M. A. G., De Kruijff, B., Kaptein, R., Bonvin, A. M. J. J., & Van Nuland, N. A. J. (2004). The nisin-lipid II complex reveals a pyrophosphate cage that provides a blueprint for novel antibiotics. Nature Structural and Molecular Biology, 11(10), 963-967. https://doi.org/10.1038/nsmb830

Arnesano, F., Banci, L., Bertini, I., & Bonvin, A. M. J. J. (2004). A docking approach to the study of copper trafficking proteins: interaction between metallochaperones and soluble domains of copper ATPases. Structure, 12(4), 669-676. https://doi.org/10.1016/j.str.2004.03.006
https://dspace.library.uu.nl/bitstream/handle/1874/42767/post-print.pdf?sequence=3

Dominguez, C., Bonvin, A. M. J. J., Winkler, G. S., van Schaik, F. M. A., Timmers, H. T. M., & Boelens, R. (2004). Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, Mutagenesis and Docking approaches. Structure, 12, 633-644. https://doi.org/10.1016/j.str.2004.03.004

Hsu, S-TD., & Bonvin, A. M. J. J. (2004). Atomic insight into the CD4 binding-induced conformational changes in HIV-1 gp120. Proteins: Structure function and bioinformatics, 55(3), 582-593. https://doi.org/10.1002/prot.20061
https://dspace.library.uu.nl/bitstream/handle/1874/42766/Hsu_Bonvin_final.pdf?sequence=3

van Drogen-Petit, A., Zwahlen, C., Peter, M., & Bonvin, A. M. J. J. (2004). Insight into molecular interactions between two PB1 domains. Journal of Molecular Biology, 336(5), 1195-1210. https://doi.org/10.1016/j.jmb.2003.12.062

Houben, K., Dominguez, C., van Schaik, F. M. A., Timmers, H. T. M., Bonvin, A. M. J. J., & Boelens, R. (2004). Solution structure of the ubiquitin-conjugating enzyme UbcH5B. Journal of Molecular Biology, 344, 513-526. https://doi.org/10.1016/j.jmb.2004.09.054

Nabuurs, S. B., Nederveen, A. J., Vranken, W., Doreleijers, J. F., Bonvin, A. M. J. J., Vuister, G. W., Vriend, G., & Spronk, C. A. E. M. (2004). DRESS: a database of refined solution NMR structures. Proteins: Structure function and bioinformatics, 55(3), 483-486. https://doi.org/10.1002/prot.20118

2003

Scholarly publications

Tzakos, AG., Fuchs, P., van Nuland, NAJ., Troganis, A., Tselios, T., Deraos, S., Deraos, G., Gerothanassis, IP., Bonvin, AMJJ., & Matsoukas, J. (2003). Structural studies and sequence homology investigations of the guinea pig myelin basic protein (MBP) epitope 74-85 analogues. Biopolymers, 71(3), 413-413.

Hsu, S-T. D., Breukink, E., Bierbaum, G., Sahl, H-G., De Kruijff, B., Kaptein, R., Van Nuland, N. A. J., & Bonvin, A. M. J. J. (2003). NMR study of mersacidin and lipid II interaction in dodecylphosphocholine micelles: Conformational changes are a key to antimicrobial activity. Journal of Biological Chemistry, 278(15), 13110-13117. https://doi.org/10.1074/jbc.M211144200

Stockner, T., Sterk, H., Kaptein, R., & Bonvin, A. M. J. J. (2003). Molecular dynamics studies of a molecular switch in the glucocorticoid receptor. Journal of Molecular Biology, 328(2), 325-334. https://doi.org/10.1016/S0022-2836(03)00316-4
https://dspace.library.uu.nl/bitstream/handle/1874/42717/Stockner_MDsimulations_2003.pdf?sequence=3

Tzakos, A. G., Bonvin, A. M. J. J., Troganis, A., Cordopatis, P., Amzel, M. L., Gerothanassis, I. P., & van Nuland, N. A. J. (2003). On the molecular basis of the recognition of angiotensin II (AII) : NMR structure of AII in solution compared with the X-ray structure of AII bound to the mAb Fab131. European Journal of Biochemistry, 270(5), 849-860.
https://dspace.library.uu.nl/bitstream/handle/1874/42786/fulltext.pdf?sequence=1

Fuchs, P., Bonvin, A. M. J. J., Bochicchio, B., Pepe, A., Alix, A. J. P., & Tamburro, A. M. (2003). Spectroscopic and theoretical characterization of the type VIII β-turn : study of the tetrapeptide GDNP. In A. M. Tamburro, & A. Pepe (Eds.), Elastin 2002 (pp. 81-88). (Didattica (chimica)). Ermes.

Linge, J. P., Williams, M. A., Spronk, C. A. E. M., Bonvin, A. M. J. J., & Nilges, M. (2003). Refinement of protein structures in explicit solvent. Proteins: Structure function and bioinformatics, 50, 496-506. https://doi.org/10.1002/prot.10299

Spronk, C. A. E. M., Nabuurs, S. B., Bonvin, A. M. J. J., Krieger, E., Vuister, G. W., & Vriend, G. (2003). The precision of NMR structure ensembles revisited. Journal of Biomolecular NMR, 25(3), 225-234. https://doi.org/10.1023/a:1022819716110

Oomen, C. J., Hoogerhout, P., Bonvin, A. M. J. J., Kuipers, B., Brughhe, H., Timmermans, H., Hasely, S. R., van Alphen, L., & Gros, P. (2003). Immunogenicity of peptide-vaccine candidates predicted by molecular dynamics simulations. Journal of Molecular Biology, 328, 1083-1089. https://doi.org/10.1016/S0022-2836(03)00377-2

Koharudin, L. M. I., Bonvin, A. M. J. J., Kaptein, R., & Boelens, R. (2003). Use of very long-distance NOEs in a fully deuterated protein: an approach for rapid protein fold determination. Journal of Magnetic Resonance, 163(2), 228-235. https://doi.org/10.1016/S1090-7807(03)00149-6
https://dspace.library.uu.nl/bitstream/handle/1874/41754/_sdarticle.pdf?sequence=1

2002

Scholarly publications

D'Amelio, N., Bonvin, AMJJ., Czisch, M., Barker, P., & Kaptein, R. (2002). The C terminus of apocytochrome b(562) undergoes fast motions and slow exchange among ordered conformations resembling the folded state. Biochemistry, 41(17), 5505-5514. https://doi.org/10.1021/bi011863n

Kalodimos, C., Bonvin, A. M. J. J., Salinas, R. K., Wechselberger, R. W., Boelens, R., & Kaptein, R. (2002). Plasticity in protein–DNA recognition: lac repressor interacts with its natural operator O1 through alternative conformations of its DNA-binding domain. EMBO Journal, 21(12), 2866-2876.
https://dspace.library.uu.nl/bitstream/handle/1874/42774/7594506a.pdf?sequence=1

D’Amelio, N., Bonvin, A. M. J. J., Czisch, M., Barker, P., & Kaptein, R. (2002). The C terminus of apocytochrome b562 undergoes fast motions and slow exchange among ordered conformations resembling the folded state. Biochemistry, 41, 5505-5514.
https://dspace.library.uu.nl/bitstream/handle/1874/44343/bi011863n.pdf?sequence=1

Hsu, S., Breukink, E. J., de Kruijff, B., Kaptein, R., Bonvin, A. M. J. J., & van Nuland, N. A. J. (2002). Mapping the targeted membrane pore formation mechanism by solution NMR: the nisin Z and lipid II interaction in SDS micelles. Biochemistry, 41, 7670-7676. https://doi.org/10.1021/bi025679t

Singh, S., Folkers, G. E., Bonvin, A. M. J. J., Boelens, R., Wechselberger, R. W., Niztayev, A., & Kaptein, R. (2002). Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli. EMBO Journal, 21(22), 6257-6266. https://doi.org/10.1093/emboj/cdf627
https://dspace.library.uu.nl/bitstream/handle/1874/42772/7594843a.pdf?sequence=1

Other output

Kalodimos, C., Bonvin, A. M. J. J., Boelens, R., & Kaptein, R. (2002). Detailed insight into the mechanisms of protein-DNA recognition. 94-96. Abstract from 4th ORCS International symposium on "Development of New Structural Biology Including Hydrogen and Hydration", Tsukuba Science City.

2001

Scholarly publications

Bonvin, AMJJ., Houben, K., Guenneugues, M., Kaptein, R., & Boelens, R. (2001). Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond N-15-C-13 ' scalar couplings ((3hb)J(NC ')). Journal of Biomolecular NMR, 21(3), 221-233. https://doi.org/10.1023/A:1012935005256

Tzakos, A., Troganis, A., Pierattelli, R., Gerothanassis, I., Bonvin, A., van Nuland, N., & Kordopatis, P. (2001). Conformational studies of angiotensin II-metal complexes by NMR spectroscopy. Journal of Inorganic Biochemistry, 86(1), 462-462.

Bonvin, A. M. J. J., Houben, K., Guenneugues, M. N. L., Kaptein, R., & Boelens, R. (2001). Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond 15N-13C’ scalar couplings (3hbJNC’). Journal of Biomolecular NMR, 21(3), 221-233. http://www.springerlink.com/
https://dspace.library.uu.nl/bitstream/handle/1874/44451/Bonvin.pdf?sequence=1

2000

Scholarly publications

Bonvin, AMJJ., Mark, AE., & van Gunsteren, WF. (2000). The GROMOS96 benchmarks for molecular simulation. Computer Physics Communications, 128(3), 550-557. https://doi.org/10.1016/S0010-4655(99)00540-8

Bonvin, A. M. J. J., Mark, A. E., & Van Gunsteren, W. F. (2000). GROMOS96 benchmarks for molecular simulation. Computer Physics Communications, 128(3), 550-557. https://doi.org/10.1016/S0010-4655(99)00540-8

Bonvin, A. M. J. J. (2000). Localisation and dynamics of sodium counterions around DNA in solution from molecular dynamics simulation. European Biophysics Journal, 29(1), 57-60. https://doi.org/10.1007/s002490050251

Bonvin, A. M. J. J., & Van Gunsteren, W. F. (2000). β-Hairpin stability and folding: Molecular dynamics studies of the first β-hairpin of tendamistat. Journal of Molecular Biology, 296(1), 255-268. https://doi.org/10.1006/jmbi.1999.3446

Van Tilborg, P. J. A., Czisch, M., Mulder, F. A. A., Folkers, G. E., Bonvin, A. M. J. J., Nair, M., Boelens, R., & Kaptein, R. (2000). Changes in dynamical behavior of the retinoid X receptor DNA-binding domain upon binding to a 14 base-pair DNA half site. Biochemistry, 39(30), 8747-8757. https://doi.org/10.1021/bi991550g

Melacini, G., Bonvin, AMJJ., Goodman, M., Boelens, R., & Kaptein, R. (2000). Hydration dynamics of the collagen triple helix by NMR. Journal of Molecular Biology, 300(5), 1041-1048. https://doi.org/10.1006/jmbi.2000.3919

van Beest, M., Dooijes, D., van de Wetering, M. L., Kjearulff, S., Bonvin, A. M. J. J., Nielsen, O., & Clevers, H. C. (2000). Sequence-specific high mobility group box factors recognize 10-12-base pair minor groove motifs. Journal of Biological Chemistry, 275(35), 27266-27273. https://doi.org/10.1074/jbc.M004102200

Oomen, C. J., Bonvin, A. M. J. J., Haseley, S. R., Hoogerhout, P., van Alphen, L., Kroon, J., & Gros, P. (2000). Rational design of a subtype-specific peptide vaccine against Neisseria meningitidis. In J. P. T. G. Barany G.B. Fields (Ed.), Peptides for a New Millenium (pp. 702-703). Kluwer Academic Publishers. https://doi.org/10.1007/0-306-46881-6_280

1999

Scholarly publications

Spronk, C. A. E. M., Bonvin, A. M. J. J., Radha, P. K., Melacini, G., Boelens, R., & Kaptein, R. (1999). The solution structure of Lac repressor headpiece 62 complexed to a symmetrical lac operator. Structure, 7(12), 1483-1492. https://doi.org/10.1016/S0969-2126(00)88339-2

1998

Scholarly publications

Bonvin, A. M. J. J., Sunnerhagen, M., Otting, G., & Van Gunsteren, W. F. (1998). Water molecules in DNA recognition II: A molecular dynamics view of the structure and hydration of the trp operator. Journal of Molecular Biology, 282(4), 859-873. https://doi.org/10.1006/jmbi.1998.2034

Sunnerhagen, M., Denisov, V. P., Venu, K., Bonvin, A. M. J. J., Carey, J., Halle, B., & Otting, G. (1998). Water molecules in DNA recognition I: Hydration lifetimes of trp operator DNA in solution measured by NMR spectroscopy. Journal of Molecular Biology, 282(4), 847-858. https://doi.org/10.1006/jmbi.1998.2033

1996

Scholarly publications

Bonvin, A., & Brünger, A. T. (1996). Do NOE distances contain enough information to assess the relative populations of multi-conformer structures? Journal of Biomolecular NMR, 7(1), 72-76.

Bonvin, A. M. J. J., Boelens, R., & Kaptein, R. (1996). Direct structure refinement using 3D NOE-NOE spectra of biomolecules. Journal of Magnetic Resonance (1969), 95(3), 626-631. https://doi.org/10.1016/0022-2364(91)90180-2

Slijper, M., Bonvin, A. M., Boelens, R., & Kaptein, R. (1996). Refined structure of lac repressor headpiece (1-56) determined by relaxation matrix calculations from 2D and 3D NOE data: change of tertiary structure upon binding to the lac operator. Journal of Molecular Biology, 259(4), 761-73. https://doi.org/10.1006/jmbi.1996.0356

1995

Scholarly publications

BONVIN, AMJJ., & BRUNGER, AT. (1995). Use of Ensemble-averaged Distance Constraints for Nmr Refinement - Validity Assessment Using Cross-validation. Journal of Cellular Biochemistry, 69-69.

Bonvin, A. M. J. J., & Brünger, A. T. (1995). Conformational variability of solution nuclear magnetic resonance structures. Journal of Molecular Biology, 250(1), 80-93. https://doi.org/10.1006/jmbi.1995.0360

SLIJPER, M., Bonvin, A., BOELENS, R., & KAPTEIN, R. (1995). Application of structure refinement using 3D NOE-NOE spectroscopy to Lac Repressor Headpiece (1-56). Journal of Magnetic Resonance - Series B, 107(3), 298-301. http://www.sciencedirect.com/science/article/pii/S1064186685710941

Van Tilborg, M. A. A., Bonvin, A. M. J. J., Hård, K., Davis, A. L., Maler, B., Boelens, R., Yamamoto, K. R., & Kaptein, R. (1995). Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by relaxation matrix calculations. Journal of Molecular Biology, 247(4), 689-700. https://doi.org/10.1016/S0022-2836(05)80148-2

1994

Scholarly publications

BONVIN, AMJJ., BOELENS, R., & KAPTEIN, R. (1994). Direct Nuclear Overhauser Effect Refinement of Crambin From 2-dimensional Nmr Data Using a Slow-cooling Annealing Protocol. Biopolymers, 34(1), 39-50. https://doi.org/10.1002/bip.360340106

BONVIN, AMJJ., BOELENS, R., & KAPTEIN, R. (1994). Time-averaged and Ensemble-averaged Direct Noe Restraints. Journal of Biomolecular NMR, 4(1), 143-149.

Bonvin, A. M. J. J., Boelens, R., & Kaptein, R. (1994). Time- and ensemble-averaged direct NOE restraints. Journal of Biomolecular NMR, 4(1), 143-149. https://doi.org/10.1007/BF00178343

Bonvin, A. M. J. J., Vis, H., Breg, J. N., Burgering, M. J. M., Boelens, R., & Kaptein, R. (1994). Nuclear magnetic resonance solution structure of the Arc repressor using relaxation matrix calculations. Journal of Molecular Biology, 236(1), 328-341. https://doi.org/10.1006/jmbi.1994.1138

Bonvin, A. M. J. J., Boelens, R., & Kaptein, R. (1994). Direct nuclear overhauser effect refinement of crambin from two- dimensional NMR data using a slow-cooling annealing protocol. Biopolymers, 34(1), 39-50.

1993

Scholarly publications

KNEGTEL, RMA., BOELENS, R., GANADU, ML., GEORGE, AVE., KATAHIRA, M., BONVIN, AMJJ., EIB, D., VANDERSAAG, PT., & KAPTEIN, R. (1993). Nmr-studies of the Human Retinoic Acid Receptor-beta Dna-binding Domain - Metal Coordination and 3-dimensional Structure. Annals of the New York Academy of Sciences, 684, 49-62. https://doi.org/10.1111/j.1749-6632.1993.tb32270.x

BONVIN, AMJJ., VIS, H., BREG, JN., BOELENS, R., & KAPTEIN, R. (1993). Relaxation Matrix Refinement of the Solution Structure of the Arc Repressor. Journal of Cellular Biochemistry, 250.

Bonvin, A. M. J. J., Rullmann, J. A. C., Lamerichs, R. M. J. N., Boelens, R., & Kaptein, R. (1993). 'Ensemble' iterative relaxation matrix approach: A new NMR refinement protocol applied to the solution structure of crambin. Proteins: Structure, Function and Genetics, 15(4), 385-400. https://doi.org/10.1002/prot.340150406

Knegtel, R. M., Boelens, R., Ganadu, M. L., George, A. V., Katahira, M., Bonvin, A. M., Eib, D., van der Saag, P. T., & Kaptein, R. (1993). NMR studies of the human retinoic acid receptor-beta DNA-binding domain. Metal coordination and three-dimensional structure. Annals of the New York Academy of Sciences, 684, 49-62.

KNEGTEL, RMA., KATAHIRA, M., SCHILTHUIS, JG., Bonvin, A., BOELENS, R., EIB, D., VANDERSAAG, PT., & KAPTEIN, R. (1993). The solution structure of the human retinoic acid receptor-beta DNA-binding domain. Journal of Biomolecular NMR, 3(1), 1-17. https://doi.org/10.1007/BF00242472

1991

Scholarly publications

Bonvin, A. M., Boelens, R., & Kaptein, R. (1991). Direct NOE refinement of biomolecular structures using 2D NMR data. Journal of Biomolecular NMR, 1(3), 305-309. https://doi.org/10.1007/BF01875523

Gonzalez, C., Rullmann, J. A. C., Bonvin, A. M. J. J., Boelens, R., & Kaptein, R. (1991). Toward an NMR R factor. Journal of Magnetic Resonance (1969), 91(3), 659-664. https://doi.org/10.1016/0022-2364(91)90397-C

1990

Scholarly publications

Burghardt, I., Di Bari, L., Bonvin, A., & Bodenhausen, G. (1990). Effects of strong coupling in multiple-quantum-filtered two-dimensional NOE spectroscopy. Journal of Magnetic Resonance (1969), 86(3), 652-656. https://doi.org/10.1016/0022-2364(90)90044-A

Prof. dr. A.M.J.J. (Alexandre) Bonvin

Prof. dr. A.M.J.J. (Alexandre) Bonvin

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1998

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1996

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1995

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1994

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1991

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1990

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