Publications

2024

V. Reys∗, Ma. Giulini∗, V. Cojocaru, A. Engel, X. Xu, J. Roel-Touris, C. Geng, F. Ambrosetti, B. Jimenez-Garcia, Z. Jandova, P.I. Koukos, C. van Noort, J.M. . Teixeira, S.C. van Keulen, M. Reau, R.V. Honorato and A.M.J.J. Bonvin. Integrative modeling in the age of machine learning: a summary of HADDOCK strategies in CAPRI rounds 47-55 BioRXiv. (2024).
K. Devantier, T.L. Toft-Bertelsen, A. Prestel, V.M.S. Kjaer, C.a Sahin, M. Giulini, S. Louka, K. Spiess, A. Manandhar, K. Qvortrup, T. Ulven, B. Hjorth Bentzen, A.M.J.J. Bonvin, N. MacAulay, B.B. Kragelund and M.M. Rosenkilde. The SH Protein of Mumps Virus is a Druggable Pentameric Viroporin. BioRXiv. 10.1101/2024.08.09.60700 (2024).
X. Xu and A.M.J.J. Bonvin Ranking protein-protein models with large language models and graph neural networks. arXiv:2407.16375 (2024).
A. Basciu, M. Athar, H. Kurt, C. Neville, G. Malloci, F. Muredda, A. Bosin, P. Ruggerone, A.M.J.J. Bonvin and A.V. Vargiu. Predicting binding events in very flexible, allosteric, multi-domain proteins. BioRXiv. 10.1101/2024.06.02.597018 (2024).
G. Bellinzona, D. Sassera and A.M.J.J. Bonvin. Accelerating Protein-Protein Interaction screens with reduced AlphaFold-Multimer sampling Bioinformatics Advances vbae153 (2024).
A. Ranaudo, M. Giulini, A. Pelissou Ayuso and A.M.J.J. Bonvin. Modelling Protein-Glycan Interactions with HADDOCK. J. Chem. Inf. Mod. 64, 7816–7825 (2024).
M. Giulini, C. Schneider, D. Cutting, N. Desai, C. Deane and A.M.J.J. Bonvin. Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking. Bioinformatics 40:btae583, p. 1-11 (2024).BioRxiv
R.V. Honorato, M.E. Trellet, B. Jiménez-García1, J.J. Schaarschmidt, M. Giulini, V. Reys, P.I. Koukos, J.P.G.L.M. Rodrigues, E. Karaca, G.C.P. van Zundert, J. Roel-Touris, C.W. van Noort, Z. Jandová, A.S.J. Melquiond and A.M.J.J. Bonvin. The HADDOCK2.4 web server: A leap forward in integrative modelling of biomolecular complexes. Nature Prot., Advanced Online Publication DOI: 10.1038/s41596-024-01011-0 (2024).
B. Vallat, B.M. Webb, J.D. Westbrook, T. Goddard, C.A. Hanke, A. Graziadei, E. Peisach, A. Zalevsky, J. Sagendorf, H. Tangmunarunkit, S. Voinea, M. Sekharan, J. Yu, A.M.J.J. Bonvin, Fr, DiMaio, G. Hummer, J. Meiler, E. Tajkhorshid, T. Ferrin, C.L. Lawson, A. Leitner, J. Rappsilber, C.A.M. Seidel, C.M. Jeffries, S.K. Burley, J. Hoch, G.i Kurisu, K.e Morris, A. Patwardhan, S. Velankar, T. Schwede, J. Trewhella, C. Kesselman, H.M. Berman, A. Sali. IHMCIF: An extension of PDBx/mmCIF data standard for integrative structure determination methods. J. Mol. Biol., 436:168546 (2024).
K.W. Collins, M.M. Copeland,, G. Brysbaert, S.J. Wodak, A.M.J.J. Bonvin, P,J, Kundrotas, I.A. Vakser and M.F. Lensink. CAPRI-Q: The CAPRI resource evaluating the quality of predicted structures of protein complexes. J. Mol. Biol., 436:168540 (2024).
M. Giulini, R.V. Honorato, J.L. Rivera, A.M.J.J. Bonvin. ARCTIC-3D: Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information. Comm. Biol. 7:49, p. 1-9 (2024).
X. Xu, A.M.J.J. Bonvin. DeepRank-GNN-esm: A Graph Neural Network for Scoring Protein-Protein Models using Protein Language Model. Bioinfo. Adv. vbad191, _Advanced Online Publication (2024).

2023

A.M.J.J. Bonvin. Empowering Global Collaboration in Structural Biology and Life Sciences. DOI:10.5281/zenodo.8135315 (2023).
M. Lensink, G. Brysbaert, N. Raouraoua, P. Bates, M. Giulini, R. Vargas Honorato, C. van Noort, J. Teixeira, A.M.J.J. Bonvin, R. Kong, H. Shi, X. Lu, S. Chang, J. Liu, Z. Guo, X. Chen, A. Morehead, R. Roy, T. Wu, N. Giri, F. Quadir, C. Chen, J. Cheng, C. Del Carpio, E. Ichiishi, L. Rodriguez-Lumbreras, J. Fernández-Recio, A. Harmalkar, L. Chu, S.Canner, R. Smanta, J. Gray, H. Li, P. Lin, J.a He, H. Tao, S. Huang, J. Roel, B. Jimenez-Garcia, C. Christoffer, A. Jain J, Y. Kagaya, H. Kannan, T. Nakamura, G. Terashi, J. Verburgt, Y. Zhang, Z. Zhang, H. Fujuta, M. Sekijima, D. Kihara, O. Khan, S. Kotelnikov, U. Ghani, D. Padhorny, D. Beglov, S. Vajda, D. Kozakov, S. Negi S, T. Ricciardelli, D. Barradas-Bautista, Z. Cao, M. Chawla, L. Cavallo, R. Oliva, R. Yin, M. Cheung, J. Guest, J. Lee, B. Pierce, B. Shor, T. Cohen, M. Halfon, D. Schneidman-Duhovny, S. Zhu, R. Yin, Y. Sun, Y. Shen, M. Maszota-Zieleniak, K. Bojarski K, E. Lubecka, M. Marcisz, A. Danielsson, L. Dziadek, M. Gaardlos, A. Giełdoń, J. Liwo, S. Samsonov, R. Slusarz, K. Zieba, A. Sieradzan, C. Czaplewski , S. Kobayashi, Y. Miyakawa, Y. Kiyota, M. Takeda-Shitaka, K. Olechnovič, L. Valančauskas, J. Dapkūnas, C. Venclovas, B. Wallner, L. Yang, C. Hou, X. He, S. Guo, S. Jiang, X. Ma, R. Duan, L. Qiu, X. Xu, X. Zou, S. Velankar, S. Wodak. Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment Proteins: Struc. Funct. & Bioinformatics 12, 1658-1683 (2023).
R. Shukla, A.J. Peoples, K.C. Ludwig, S. Maity, M.G.N. Derks, S. de Benedetti, A.M. Krueger, B.J.A. Vermeulen, F. Lavore, R.V. Honorato, F. Grein, A.M.J.J. Bonvin, U. Kubitscheck, E. Breukink, C. Achorn, A. Nitti, C.J. Schwalen, A.L. Spoering, L.L. Ling, D. Hughes, M. Lelli, W.H. Roos, K. Lewis, T. Schneider, M. Weingarth. A new antibiotic from an uncultured bacterium binds to an immutable target. Cell 186, 4059-4073, DOI:10.1016/j.cell.2023.07.038 (2023).
F. van der Krift, D.W. Zijlmans, R. Shukla, A. Javed, P.I. Koukos, L.L.E. Schwarz, E.P.M. Timmermans-Sprang, P.E.M. Maas, D. Gahtory, M. van den Nieuwboer, J.A. Mol, G.J. Strous, A.M.J.J. Bonvin, M. van der Stelt, E.J.A. Veldhuizen, M.s Weingarth, M. Vermeulen, J. Klumperman, M.M. Maurice. A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance. Life Science Alliance 6 e202302058; DOI: 10.26508/lsa.202302058 (2023).
S. van Keulen and A.M.J.J. Bonvin. Improving the Quality of Co-evolution Intermolecular Contact Prediction with DisVis. Proteins: Struc. Funct. & Bioinformatics 91, 1407-1416 (2023). Preprint here.
H. Schweke, Q. Xu, G. Tauriello, L. Pantolini, T. Schwede, F. Cazals, A. Lhéritier, J. Fernandez-Recio, L.A. Rodríguez-Lumbreras, O. Schueler-Furman, J.K. Varga, B. Jiménez-García, M.F. Réau, A.M.J.J. Bonvin, C. Savojardo, P.-L. Martelli, R. Casadio, J. Tubiana, H. Wolfson, R. Oliva, D. Barradas-Bautista, T. Ricciardelli, L. Cavallo, Č. Venclovas, K. Olechnovič, R. Guerois, J. Andreani, J. Martin, X. Wang, D. Kihara , A. Marchand, B. Correia, X. Zou, S. Dey, R. Dunbrack, E. Levy, S. Wodak. Discriminating physiological from non-physiological interfaces in structures of protein complexes: a community-wide study. Proteomics 23, 1-21 (2023).
M.F. Réau, N.Renaud, L.C. Xue and A.M.J.J. Bonvin. DeepRank-GNN: A Graph Neural Network Framework to Learn Patterns in Protein-Protein Interfaces. Bioinformatics 39, btac759, 1-8 (2023). Preprint here.
F. Ambrosetti, Z. Jandova and A.M.J.J. Bonvin. A protocol for information-driven antibody-antigen modelling with the HADDOCK2.4 webserver. Methods in molecular biology 2552, 267-282 (2023). Preprint.
Y. Jung, C. Geng, A.M.J.J. Bonvin, L.C. Xue, V.G. Honavar. MetaScore: A novel machine-learning based approach to improve traditional scoring functions for scoring protein-protein docking conformations. Biomolecules, 13, 121 (1-200) (2023). Preprint here).

2022

M.J. Abraham, R. Apostolov, P. Bauer, A.M.J.J. Bonvin, J.M. Correia Teixeira, B.L. de Groot, V. Gapsys, G. Groenhof, B. Hess, E. Laure, E. Lindahl, A.S.J. Melquiond, D. Morozov, J.P.G.L.M. Rodrigues, M. Trellet, R. Vargas Honorato. BioExcel Updated Whitepaper on Scientific Software Development. Zenodo https://doi.org/10.5281/zenodo.6404474 (2022).
M. Stahl Madsen, M. Broekema, M. Rønn Madsen, A. Koppen, A. Borgman, C. Gräwe, E. Thomsen, D. Westland, M. Kranendonk, M. Groot Koerkamp, N. Hamers, A.M.J.J. Bonvin, J. Ramos Pittol, K. Natarajan, S. Kersten, F. Holstege, H. Monajemi, S. van Mil, M. Vermeulen, B. Kragelund, D. Cassiman, S. Mandrup and E. Kalkhoven. PPARγ lipodystrophy mutants reveal intermolecular interactions required for enhancer activation. Nature Comm., 13, 7090 (2022).
A. Basciu, L. Callea, S. Motta, A.M.J.J. Bonvin, L. Bonati and A.V. Vargiu. No dance, no partner! A tale of receptor flexibility in docking and virtual screening. Annual Reports in Medicinal Chemistry (2022)
R. Shukla, F. Lavore, So. Maity, M.G.N. Derks, C.R. Jones4, B.J.A. Vermeulen, A. Melcrová, M.A. Morris, L.M. Becker, X. Wang, R. Kumar, J. Medeiros-Silva, R.A.M. van Beekveld, A.M.J.J. Bonvin, J. Lorent, M. Lelli, J. Nowick, H.D. MacGillavry, A.J. Peoples, A.L. Spoering, L.L. Ling, D.E. Hughes, W.H. Roos, E. Breukink, K. Lewis and M. Weingarth. Teixobactin kills bacteria by a two-pronged attack on the cell envelope. Nature 608, 390-396 (2022)
C.J. Buchanan, B. Gaunt, P.J. Harrison, Y. Yang, J. Liu, A. Khan, A.M. Giltrap, A. Le Bas, P.N. Ward, K. Gupta, M. Dumoux, T.K. Tan, L. Schimaski, S. Daga, N. Picchiotti, M. Baldassarri, E. Benetti, C. Fallerini, F. Fava, A. Giliberti, P.I. Koukos, M.J. Davy, A. Lakshminarayanan, X. Xue, G. Papadakis, L.P. Deimel, V. Casablancas-Antràs, T.D.W. Claridge, A.M.J.J. Bonvin, Q.J. Sattentau, S. Furini, M. Gori, J.Huo, R.J. Owens, C. Schaffitzel, I. Berger, A. Renieri, GEN-COVID Multicenter Study, J.H. Naismith, A. Baldwin, B.G. Davis. Pathogen-sugar interactions revealed by universal saturation transfer analysis. Science 377, 385(1-17) (2022).
V. Charitou, S.C. van Keulen and A.M.J.J. Bonvin. A Cyclisation and Docking Protocol for Cyclic Peptide-Protein Modelling using HADDOCK2.4. J. Chem. Theory Comput. 18, 4027–4040 (2022).
B. Garofalo, A.M.J.J. Bonvin, A. Bosin, F.P. Di Giorgio, R. Ombrato and A.V. Vargiu. Molecular Insights Into Binding and Activation of the Human KCNQ2 Channel by Retigabine. Frontiers Mol. Biosci. 9, 839249 (2022).
N. Rosário-Ferreir, A.M.J.J. Bonvin and Irina S. Moreira. Using machine-learning-driven approaches to boost hot-spot’s knowledge. WIREs Comp. Mol. Sci., 12, e1602 (2022).
T Neijenhuis, S.C. van Keulen and A.M.J.J. Bonvin. Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4. Structure 30, 476-484 (2022).

2021

G. Dudas, S. Hong, B. Potter, S. Calvignac-Spencer, F. Niatou-Singa, T. Tombolomako, T. Fuh-Neba, U. Vickos, M. Ulrich, F. Leendertz, K. Khan, C. Huber, A. Watts, I. Olendraitė, J. Snijder, K. Wijnant, A.M.J.J. Bonvin, P. Martres, S. Behillil, A. Ayouba, M. Maidadi, D. Djomsi, C. Godwe, C. Butel, A. Šimaitis, M. Gabrielaite, M. Katėnaitė, R. Norvilas, L. Raugaitė, G. Koyaweda, J. Kaleb Kandou, R. Jonikas, I. Nasvytienė, Ž. Žemeckienė, D. Gečys, K. Tamušauskaitė, M. Norkienė, E. Vasiliūnaitė, D. Žiogienė, A. Timinskas, M. Šukys, M. Šarauskas, G. Alzbutas, A. Amuri, E. Lusamaki, J. Makangara, F. Muyembe, E. Lofiko, P. Mbala, J. Muyembe-Tamfum, M. Darnycka Belizaire, R. Essomba, M. Claire Assoumou, A. Mboringong, A. Baba Dieng, D. Juozapaitė, S. Hosch, J. Obama, M. Ondo’o Ayekaba, D. Naumovas, A. Pautienius, C. Rafaï, A. Vitkauskienė, R. Ugenskienė, A. Gedvilaitė, D. Čereškevičius, V. Lesauskaitė, L. Žemaitis, L. Griškevičius and G. Baele. Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletion. Nature Comm. 12, 5769 (2021). Preprint available here.
M.F. Lensink, G. Brysbaert, T. Mauri, N. Nadzirin, S. Velankar, R.A.G. Chaleil, T. Clarence, P.A. Bates, R. Kong, B. Liu, G. Yang, M. Liu, H. Shi, X. Lu, S. Chang, R.S. Roy, F. Quadir, J. Liu, J. Cheng, A. Antoniak, C. Czaplewski, A. Giełdoń, M. Kogut, A.G. Lipska, A. Liwo, E.A. Lubecka, M. Maszota-Zieleniak, A.K. Sieradzan, R. Ślusarz, P.A. Wesołowski, K. Zięba, C.A. Del Carpio Muñoz, E. Ichiishi, A. Harmalkar, J.J. Gray, A.M.J.J. Bonvin, F. Ambrosetti, R. Vargas Honorato, Z. Jandova, B. Jiménez-García, P.I. Koukos, S. Van Keulen, C.W. Van Noort, M. Réau, J. Roel-Touris, S. Kotelnikov, D. Padhorny, K.A. Porter, A. Alekseenko, M. Ignatov, I. Desta, R. Ashizawa, Z. Sun, U. Ghani, N. Hashemi, S. Vajda, D. Kozakov, M. Rosell, L.A. Rodríguez-Lumbreras, J. Fernandez-Recio, A. Karczynska, S. Grudinin, Y. Yan, H. Li, P. Lin, S. Huang, C. Christoffer, G. Terashi, J. Verburgt, D. Sarkar, T. Aderinwale, X. Wang, D. Kihara, T. Nakamura, Y. Hanazono, R. Gowthaman, J.D. Guest, R. Yin, G. Taherzadeh, B.G. Pierce, D. Barradas-Bautista, Z. Cao, L. Cavallo, R. Oliva, Y. Sun, S. Zhu, Y. Shen, T. Park, H. Woo, J. Yang, S. Kwon, J. Won, C. Seok, Y. Kiyota, S. Kobayashi, Y. Harada, M. Takeda-Shitaka, P.J. Kundrotas, A. Singh, I.A. Vakser, J. Dapkūnas, . Olechnovič, Č. Venclovas, R. Duan, L. Qiu, X. Xu, S. Zhang, X. Zou, S.J. Wodak. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins: Struc. Funct. & Bioinformatics, 89, 1800-1823 (2021).
R. Vargas Honorato, P.I. Koukos, B. Jimenez-Garcia, A. Tsaregorodtsev, M. Verlato, A. Giachetti, A. Rosato and A.M.J.J. Bonvin. Structural biology in the clouds: The WeNMR-EOSC Ecosystem. Frontiers Mol. Biosci. 8, fmolb.2021.729513 (2021).
P.I. Koukos, M.F. Reau and A.M.J.J. Bonvin. Shape-restrained modelling of protein-small molecule complexes with HADDOCK. J. Chem. Inf. and Mod. 61, 4807–4818 (2021). BioRxiv preprint available here.
A.M.J.J. Bonvin. 50 years of PDB: A catalyst in structural biology. Nature Methods 18, 448–449 (2021).
U.B. le Paige, S. Xiang, M.M.R.M. Hendrix, Y. Zhang., G.E. Folkers, M. Weingarth, A.M.J.J. Bonvin, T.G. Kutateladze, I.K.Voets, M. Baldus and H. van Ingen. Characterization of nucleosome sediments for protein interaction studies by solid-state NMR spectroscopy. Magn. Reson., 2, 105-116 (2021).
Z. Jandova, A.V. Vargiu and A.M.J.J. Bonvin. Native or non-native protein-protein docking models? Molecular dynamics to the rescue. J. Chem. Theo. and Comp. 17, 5944−5954 (2021).
C.W. van Noort, R.V. Honorato and A.M.J.J. Bonvin. Information-Driven Modeling of Biomolecular Complexes. Curr. Opin. Struct. Biol. 70, 70-77 (2021).
P. Matos-Filipe, A.J. Preto, P.I. Koukos, J. Mourão, A.M.J.J. Bonvin and I.S. Moreira. MENSADB: A Thorough Structural Analysis of Membrane Protein Dimers. Database, doi:10.1093/database/baab013, 1-10 (2021).
N.Renaud, C. Geng, S. Georgievska, F. Ambrosetti, L. Ridder, D.F Marzella, M.F. Réau, A.M.J.J. Bonvin and L.C. Xue. DeepRank: A deep learning framework for data mining 3D protein-protein interfaces. Nature Comm. 12, 7068 (2021).
S. Nizamuddin, S. Koidl, T. Bhuiyan, T.V. Werner, M.L. Biniossek, A.M.J.J. Bonvin, S. Lassmann and H.Th.M. Timmers. Integrating quantitative proteomics with accurate genome profiling of transcription factors by greenCUT&RUN. Nucl. Acids Res. 49, e49-‌e49 (2021).
O.M.H. Salo-Ahen#, I. Alanko, R. Bhadane, A.M.J.J. Bonvin#, R. Vargas Honorato, S. Hossain, A.H. Juffer, A. Kabedev, M. Lahtela-Kakkonen, A. Støttrup Larsen, E. Lescrinier, P. Marimuthu, M.. Mirza, G. Mustafa, A. Nunes-Alves#, T. Pantsar, A. Saadabadi, K. Singaravelu, M. Vanmeert. Molecular dynamics simulations in drug discovery and pharmaceutical development. Processes. 9, 71 (2021).
B. Jiménez-García, J.M.C. Teixeira, M.E. Trellet, J.P.G.L.M. Rodrigues and A.M.J.J. Bonvin. PDB-Tools Web: A user-friendly interface for the manipulation of PDB files Proteins: Struc. Funct. & Bioinformatics, 89, 330-335 (2021).

2020

A. Saponaro, V. Maione, A.M.J.J. Bonvin and F. Cantini. Understanding Docking Complexes of Macromolecules Using HADDOCK: The Synergy between Experimental Data and Computations. Bio-protocol 10, e3793 (2020).
M. Schwarz, P. Skrinjar, M.J. Fink, S. Kronister, T. Mechtler, P.I. Koukos, A.M.J.J. Bonvin, D. Kasper and H. Mikula. A click-flipped enzyme substrate boosts the performance of the diagnostic screening for Hunter syndrome. Chem. Sci., 10.1039/D0SC04696E (2020).
C.Y.L. Lau, F, Fontana, L, Mandemaker, D, Wezendonk, B, Vermeer, A.M.J.J. Bonvin, R. de Vries, H. Zhang, K. Remaut, J. van den Dikkenberg, J. Silva, A. Hassan, B. Perrone, R. Kuemmerle, F. Gelain, W. Hennink, M. Weingarth, and E. Mastrobattista. Control over the fibrillization yield by varying the oligomeric nucleation propensities of self-assembling peptides. Comm. Chem. 3, 164 (2020).
V. Tozzini , G. Palermo , A.M.J.J. Bonvin , M. Dal Peraro and R.E. Amaro. Editorial: Multiscale Modeling from Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations. Front. Mol. Biosci. 10.3389/fmolb.2020.00194 (2020).
J.L. Roel-Touris, B. Jiménez-García and A.M.J.J. Bonvin. Integrative Modeling of Membrane-associated Protein Assemblies. Nature Comm., 11, 6210 (2020).
H.H. Rabouw, L.J. Visser, T.C. Passchier, M.A. Langereis, F. Liu, P. Giansanti, A.L.W. van Vliet, J.G. Dekker, S.G. van der Grein, J.G. Saucedo, A.A. Anand, M.E. Trellet, A.M.J.J. Bonvin, P. Walter, A.J.R. Heck, R.J. de Groot and F.J.M. van Kuppeveld. Inhibition of the integrated stress response by viral proteins that block p-eIF2–eIF2B association. Nature Microbiology, 58, 1361-1373 (2020).
A. Leitner, A.M.J.J. Bonvin, C.H. Borchers, R.J. Chalkley, . Chamot-Rooke, C.W. Combe, J. Cox, M. Dong, L. Fischer, M. Götze, F.C. Gozzo, A.J.R. Heck, M.R. Hoopmann, L. Huang, Y. Ishihama, A.R. Jones, N. Kalisman, O. Kohlbacher, K. Mechtler, R.L. Moritz, E. Netz, P.r Novak, E. Petrotchenko, A. Sali, R.A. Scheltema, C. Schmidt, D. Schriemer, A. Sinz, F. Sobott, F. Stengel, K. Thalassinos, H. Urlaub, R. Viner, J.A. Vizcaino, M. R. Wilkins, J. Rappsilber. Towards Increased Reliability, Transparency and Accessibility in Crosslinking Mass Spectrometry Structure, 28, 1259-1268 (2020).
J. Roel-Touris and A.M.J.J. Bonvin. Coarse-Grained (Hybrid) Integrative Modeling of Biomolecular Interactions. Comp. Struct. Biotech. J., 18, 1182-1190 (2020).
R. Shukla, J. Medeiros-Silva, A. Parmar, B.J.A. Vermeulen, S. Das, A. Paioni, S. Jekhmane, J. Lorent, A.M.J.J. Bonvin, M. Baldus, M. Lelli, E.J.A. Veldhuizen, E. Breukink, I. Singh and M. Weingarth. Mode of action of teixobactins in cellular conditions. Nature Communications, 11, 2848 (2020).
C. Orengo, S. Velankar, S. Wodak, V. Zoete, A.M.J.J. Bonvin, A. Elofsson, K.A Feen.stra, D.L. Gerloff, T. Hamelryck, J.M. Hancock, M. Helmer-Citterich, A. Hospital, M. Orozco, A. Perrakis, M. Rarey, C. Soares, J.L. Sussman, J.M. Thornton, P. Tuffery, G. Tusnady, R. Wierenga, T. Salminen, B. Schneider. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). F1000 Research, Awaiting peer review (2020).
N. Renault, Y. Jung, V. Honavar, C. Geng, A.M.J.J. Bonvin and L. Xue. 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 (2020).
F. Ambrosetti, T.H. Olsed, P.P. Olimpieri, B. Jiménez-García, E. Milanetti, P. Marcatilli and A.M.J.J. Bonvin. proABC-2: PRediction Of AntiBody Contacts v2 and its application to information-driven docking. Bioinformatics, 36, 5107–5108 (2020).
C. van Leeuwen, D. Podareanu, V. Codreanu, M. Cai, A. Berg, S. Portegies Zwart, R. Stoffer, M. Veerman, C. van Heerwaarden, S. Otten, S. Caron, C. Geng, F. Ambrosetti, A.M.J.J. Bonvin. Deep-learning enhancement of large scale numerical simulations. Whitepaper (2020).
K. Elez, A.M.J.J. Bonvin#, Anna Vangone#. Biological vs crystallographic protein interfaces: An overview of computational approaches for their classification. Crystals, 10, 114 (2020).
P.I. Koukos, J. Roel-Touris, F. Ambrosetti, C. Geng, J. Schaarschmidt, M.E. Trellet, A.S.J. Melquiond, L.C. Xue, R.V. Honorato, I. Moreira, Z. Kurkcuoglu, A. Vangone and A.M.J.J. Bonvin. An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45. Proteins: Struc. Funct. & Bioinformatics, 88, 1029-1036 (2020).
F. Ambrosetti, B. Jiménez-García, J. Roel-Touris and A.M.J.J. Bonvin. Modeling Antibody-Antigen Complexes by Information-Driven Docking. Structure, 28, 119-129 (2020). Preprint freely available from here.
Z. Kurkcuoglu and A.M.J.J. Bonvin. Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems. Proteins: Struc. Funct. & Bioinformatics, 88, 292-306 (2020).
T. Lawson, S. El-Kamand, D. Boucher, D. Cong Duong, R. Kariawasam, A.M.J.J. Bonvin, D.J. Richard, R. Gamsjaeger1 and Liza Cubeddu. The structural details of the interaction of single-stranded DNA binding protein hSSB2 (NABP1/OBFC2A) with UV-damaged DNA. Proteins: Struc. Funct. & Bioinformatics, 88, 319-326 (2020).
A. Basciu, P.I. Koukos, G. Malloci, A.M.J.J. Bonvin and A.V. Vargiu. Coupling enhanced sampling of the apo‐receptor with template‐based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4. J. Comp. Aid. Mol. Des. 34, 149-162 (2020). A preprint can be downloaded from here.
J.L. Roel Touris, A.M.J.J. Bonvin and B. Jimenez-Garcia. LightDock goes information-driven. Bioinformatics, 36, 950–952 (2020).
M.E. Trellet, G. van Zundert and A.M.J.J. Bonvin. Protein-protein modelling using cryo-EM restraints. In: Structural Bioinformatics. Methods in Molecular Biology, vol 2112. Humana, New York, NY, (2020). A preprint is available here.
P.I. Koukos and A.M.J.J. Bonvin. Integrative modelling of biomolecular complexes. J. Mol. Biol. 432, 2861-2881 (2020)
C. Geng, Y. Jung, N. Renaud, V. Honavar, A.M.J.J. Bonvin and L.C. Xue. iScore: A novel graph kernel-based function for scoring protein-protein docking models Bioinformatics 36, 112–121 (2020).

2019

M.F. Lensink, G. Brysbaert N. Nadzirin, S. Velankar, R.A.G. Chaleil, T, Gerguri, P.A. Bates, E. Laine, A. Carbone, S. Grudinin, R. Kong, R. Liu, X. Xu, H, Shi, S. Chang, M. Eisenstein, A.a Karczynska, C. Czaplewski, E. Lubecka, A. Lipska, P. Krupa, M. Mozolewska, L. Golon, S. Samsonov, A. Liwo, S. Crivelli, G. Pagès, M. Karasikov, M. Kadukova, Y. Yan, S. Huang, M. Rosell, L.A. Rodríguez‐Lumbreras, M. Romero‐Durana, L. Díaz‐Bueno, J. Fernandez‐Recio, C. Christoffer, G. Terashi, W. Shin, T. Aderinwale, S. Raghavendra Maddhuri Venkata Subraman, D. Kihara, D. Kozakov, S. Vajda, K. Porter, D. Padhorny, I. Desta, D. Beglov, M. Ignatov, S. Kotelnikov, I.H. Moal, D.W. Ritchie, I. Chauvot de Beauchêne, B. Maigret, M. Devignes, M.E. Ruiz Echartea, D, Barradas‐Bautista, Z. Cao, L. Cavallo, R. Oliva, Y. Cao, Y. Shen, M. Baek, T. Park, H. Woo, C. Seok, M. Braitbard, L. Bitton, D. Scheidman‐Duhovny, J. Dapkūnas, K. Olechnovič, Č. Venclovas, P.J. Kundrotas, S. Belkin, D. Chakravarty, V.D. Badal, I.A. Vakser, T.Vreven, S. Vangaveti, T. Borrman, Z. Weng, J.D. Guest, R. Gowthaman, B.G. Pierce, X. Xu, R. Duan, L. Qiu, J. Hou, B. Ryan Merideth, Z. Ma, J. Cheng, X. Zou, P.I. Koukos, J. Roel‐Touris, . Ambrosetti, C. Geng. J. Schaarschmidt, M.E. Trellet, A.S.J. Melquiond, L. Xue, B. Jiménez‐Garcí, C.W. van Noort, R.V. Honorato, A.M.J.J. Bonvin, S.J. Wodak. Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment. Proteins: Struc. Funct. & Bioinformatics, 87, 1200-1221 (2019)
H.M. Berman, P,D. Adams, A.M.J.J. Bonvin, S.K. Burley, B. Carragher, W. Chiu, F. DiMaio, T.E. Ferrin, M.J. Gabanyi, T.D. Goddard, P.R. Griffin, J. Haas, C.A. Hanke, J.C. Hoch, G. Hummer, G. Kurisu, C.L. Lawson, A. Leitner, J.L. Markley, J. Meiler, G.T. Montelione, G.N. Phillips Jr., T. Prisner, J. Rappsilber, D.C. Schriemer, T. Schwede, C.A.M. Seidel, T.S. Strutzenberg, D.I. Svergun, E. Tajkhorshid, J. Trewhella, B. Vallat, S. Velankar, G.W. Vuister, B. Webb, J.D. Westbrook, K.L. White, A. Sali. Federating Sructural Models and Data: Outcomes from a Workshop on Archiving Integrative Structures. Structure 27, 1745-1759 (2019).
M. Abraham, R. Apostolov, J. Barnoud, P. Bauer, C. Blau, A.M.J.J. Bonvin, M. Chavent, J. Chodera, K. Čondić-Jurkić, L. Delemotte, H. Grubmüller, R. Howard, E.J. Jordan, E. Lindal, O.H.S. Ollila, J. Selent, D. Smith, P. Stansfeld, J. Tiemann, M. Trellet, C. Woods and A. Zhmurov. Sharing Data from Molecular Simulations. J. Chem. Inf. and Model. 59, 4093-4099 (2019).
R.V. Honorato, J. Roel-Touris and A.M.J.J. Bonvin. MARTINI-based protein-DNA coarse-grained HADDOCKing. Frontiers in Molecular Biosciences, 6, 102 (2019).
J. Roel-Touris, C.G. Don, R.V. Honorato, J.P.G.L.M Rodrigues and A.M.J.J. Bonvin. Less is more: Coarse-grained integrative modeling of large biomolecular assemblies with HADDOCK. J. Chem. Theo. and Comp., 15, 6358-6367 (2019).
R.A. Norman, F. Ambrosetti, A.M.J.J. Bonvin, L.J. Colwell, S. Kelm, S. Kumar and K. Krawczyk. Computational approaches to therapeutic antibody design: established methods and emerging trends. Briefings in Bioinformatics, bbz095 (2019).
L. Goldbach, B. Vermeulen, S. Caner, M. Liu, C.Tysoe, L. van Gijzel, R. Yoshisada, M.E. Trellet, H. van Ingen, G. Brayer, A.M.J.J. Bonvin and S. Jongkees. Folding Then Binding vs. Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic alpha-Amylase. ACS Chemical Biology 14, 1751-1759 (2019).
B. Jiménez-García, K. Elez, P.I. Koukos, A.M.J.J. Bonvin and A. Vangone. PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes. Bioinformatics, 35, 4821–4823 (2019).
A. Basciu, G. Malloci, F. Pietrucci, A.M.J.J. Bonvin and A.V. Vargiu. Holo-like and druggable protein conformations from enhanced-sampling of binding pocket shape. J. Chem. Inf. and Mod., 59, 1515–1528 (2019).
C. Morris, P. Andreetto, L. Banci, A.M.J.J. Bonvin, G.G. Chojnowski, L. del Cano, J.M. Carazo; P. Conesa, S. Daenke, G. Damaskos, A. Giachetti, N. Haley, M. Hekkelman, P. Heuser, R. Joosten, D. Kouřil, A. Křenek, T. Kulhánek, V. Lamzin, N. Nadzirin, A. Perrakis, A. Rosato, F. Sanderson, J. Segura, J. Schaarschmidt, E. Sobolev, S. Traldi, M.E. Trellet, S, Velankar, M. Verlato, and M. Winn. West-Life: A Virtual Research Environment for structural biology. Journal of Structural Biology: X, 1, 100006 (2019).
C. Geng. Li J. Roel-Touris and A.M.J.J. Bonvin. Finding the ∆∆G spot: Are predictors of binding affinity changes upon mutations in protein-protein interactions ready for it? WIREs Computational Molecular Science 9, e1410 (2019).
C. Geng, A. Vangone, G.E. Folkers, L.C. Xue and A.M.J.J. Bonvin. iSEE: Interface Structure, Evolution and Energy-based machine learning predictor of binding affinity changes upon mutations. Proteins: Struc. Funct. & Bioinformatics 87, 110-119 (2019).
P.I. Koukos, L.C. Xue and A.M.J.J. Bonvin. Protein-ligand pose and affinity prediction. Lessons from D3R Grand Challenge 3. J. Comp. Aid. Mol. Des. 33, 83-91 (2019).
M.F. Broekema, M.P.G. Massink, C. Donato, J. de Ligt, J. Schaarschmidt, M.G. Schooneman, F.S. van Nierop, D. Melchers, M.N. Gerding, R. Houtman, A.M.J.J. Bonvin, A.R. Majithia, H. Monajemi, G.W. van Haaften, M.R. Soeters and E. Kalkhoven. Natural helix 9 mutants of PPARγ differently affect its transcriptional activity. Molecular Metabolism 20, 115-127 (209).

2018

A. Vangone#, J. Schaarschmidt, P. Koukos, C. Geng, N. Citro, M.E. Trellet, L.C. Xue and A.M.J.J. Bonvin. Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server. Bioinformatics, 35, 1585–1587 (2018).
J.P.G.L.M. Rodrigues, J.M.C. Teixeira, M.E. Trellet and A.M.J.J. Bonvin. pdb-tools: a swiss army knife for molecular structures. F1000Research, 7:1961 (2018)
P.I. Koukos, I. Faro, C.W. van Noort and A.M.J.J. Bonvin. A membrane protein complex docking benchmark. J. Mol. Biol. 430, 5246-‌5256 (2018).
W. Roseboom, M.G. Nazir, N.Y. Meiresonne, T. Mohammadi, J. Verheul, H. Buncherd, A.M.J.J. Bonvin, L.J. de Koning, C.G. de Koster, L. de Jong, T. Den Blaauwen. 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, 2928 (2018).
D. Salomoni, I. Campos, L. Gaido, J. Marco de Lucas, P. Solagna, J. Gomes, L. Matyska, P. Fuhrman, M. Hardt, G. Donvito, L. Dutka, M. Plociennik, R. Barbera, I. Blanquer, A. Ceccanti, E. Cetinic, M. David, C. Duma, A. López-García, G. Moltó, P. Orviz, Z. Sustr, M. Viljoen, F. Aguilar, L. Alves, M. Antonacci, L. A. Antonelli, S. Bagnasco, A.M.J.J. Bonvin, R. Bruno, Y. Chen, A. Costa, D. Davidovic, B. Ertl, M. Fargetta, S. Fiore, S. Gallozzi, Z. Kurkcuoglu, L. Lloret, J. Martins, A. Nuzzo, P. Nassisi, C. Palazzo, J. Pina, E. Sciacca, D. Spiga, M. Tangaro, M. Urbaniak, S. Vallero, B. Wegh, V. Zaccolo, F. Zambelli, T. Zok. INDIGO-DataCloud: a Platform to Facilitate Seamless Access to E-Infrastructures. J. Grid. Comp. 16, 381-408 (2018).
K. Elez, A.M.J.J. Bonvin* and A. Vangone. Distinguishing crystallographic from biological interfaces in protein complexes: Role of intermolecular contacts and energetics for classification. BMC Bioinformatics, 19 (Suppl 15), 438 (2018).
A.M.J.J. Bonvin, E. Karaca, P.L. Kastritis & J.P.G.L.M. Rodrigues. Correspondence: Defining distance restraints in HADDOCK. Nature Protocols 13, 1503 (2018). Free online only access
M.J. Abraham, A.S.J. Melquiond, E. Ippoliti, V. Gapsys, B. Hess, M. Trellet, J.P.G.L.M. Rodrigues, E. Laure, R. Apostolov, B.L. de Groot, A.M.J.J. Bonvin, E. Lindahl. BioExcel Whitepaper on Scientific Software Development. Zenodo https://doi.org/10.5281/zenodo.1194634 (2018).
A.M.J.J. Bonvin, C. Geng, M. van Dijk, E. Karaca, P. L. Kastritis, P.I. Koukos, Z. Kurkcuoglu, A.S.J. Melquiond, J.P.G.L.M. Rodrigues, J. Schaarschmidt, C. Schmitz, J. Roel-Touris, M.E. Trellet, S. de Vries, A. Vangone, L. Xue, G.C.P. van Zundert HADDOCK. In Encyclopedia of Biophysics, In press (2018).
A.J. Preto, J.G. Almeida, J. Schaarschmidt, L.C. Xue, I.S. Moreira and A.M.J.J. Bonvin. Computational tools for the structural characterization of proteins and their complexes from sequence-evolutionary data. In: Roberts G., Watts A., European Biophysical Societies (eds) Encyclopedia of Biophysics. Springer, Berlin, Heidelberg (2018),
S. Narasimhan, D. Mance, C. Pinto, M. Weingarth, A.M.J.J. Bonvin and Marc Baldus. Rapid Prediction of Multi-dimensional NMR Data Sets Using FANDAS. In: Methods in Molecular Biology: Protein NMR Humana Press, New York, NY, 111-132 (2018).
J. Schaarschmidt, B. Monastyrskyy, A.y Kryshtafovych and A.M.J.J. Bonvin. Assessment of Contact Predictions in CASP12: Co-Evolution and Deep Learning Coming of Age. Proteins: Struc. Funct. & Bioinformatics 86(S1), 51-66 (2018).
Z. Kurkcuoglu, P.I. Koukos, N. Citro, M.E. Trellet, J.P.G.L.M. Rodrigues, I.S. Moreira, J. Roel-Touris, A.S.J. Melquiond, C. Geng, J. Schaarschmidt, L.C. Xue, A. Vangone and A.M.J.J. Bonvin. Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. J. Comp. Aid. Mol. Des. 32, 175-185 (2018).

2017

A. Vangone and A.M.J.J. Bonvin. PRODIGY: A Contact-based Predictor of Binding Affinity in Protein-protein Complexes. Bio-protocol 7, e2124, DOI:10.21769/BioProtoc.2124 (2017)
E. Karaca, J.P.G.L.M. Rodrigues, A. Graziadei, A.M.J.J. Bonvin and T. Carlomagno. An Integrative Framework for Structure Determination of Molecular Machines. Nature Methods 14, 897-902 (2017).
I.S. Moreira, P.I. Koukos, R. Melo, J.G. Almeida, A.J. Preto, J. Schaarschmidt, M. Trellet, Z.H. Gümüş, J. Costa and A.M.J.J. Bonvin. SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots. Sci. Reports. 7:8007 (2017).
J.G. Almeida, A.J. Preto, P.I. Koukos, A.M.J.J. Bonvin and I.S. Moreira. Membrane proteins structures: A review on computational modeling tools. Biochimica et Biophysica Acta (BBA) - Biomembranes. 1859, 2021-2039 (2017).
K.M. Visscher, J. Medeiros-Silva, D. Mance, J.P.G.L.M. Rodrigues, M. Daniëls, A.M.J.J. Bonvin, M. Baldus, and M. Weingarth. A study on the supramolecular organization of K+ channel clusters in membranes. Angew. Chem. Intl. 56, 13222-13227 (2017).
A. Vangone, R. Oliva, L. Cavallo and A.M.J.J. Bonvin. Prediction of Biomolecular Complexes. In: From Protein Structure to Function with Bioinformatics. Ed. Daniel John Rigden, Springer, 160-167 (2017).
C. Geng, S. Narasimhan, J. P.G.L.M. Rodrigues and A.M.J.J. Bonvin. Information-driven, ensemble flexible peptide docking using HADDOCK. Methods in Molecular Biology: Modeling Peptide-Protein Interactions. Eds Ora Schueler-Furman and Nir London. Humana Press Inc. 1561, 109-138 (2017).
R.C.G. de Bruin, A.G.M. Stam, A. Vangone, P. van Bergen en Henegouwen, H.M.W. Verheul, A.M.J.J. Bonvin, T.D. de Gruijl, H.J. van der Vliet. Prevention of Vγ9Vδ2-T cell activation by a Vγ9Vδ2-TCR nanobody. Journal of Immunology, 198, 308-317 (2017).
T. Bohnuud, L. Luo, S.J. Wodak, A.M.J.J. Bonvin, Z. Weng, S. Vajda, O. Schueler-Furman and D. Kozakov. A benchmark testing ground for integrating homology modeling and protein docking. Proteins: Struc. Funct. & Bioinformatics, 85, 10-17 (2017).
G.C.P. van Zundert, M. Trellet, J. Schaarschmidt, Z. Kurkcuoglu, M. David, M. Verlato, A. Rosato and A.M.J.J. Bonvin. The DisVis and PowerFit web servers: Explorative and Integrative Modeling of Biomolecular Complexes. J. Mol. Biol., 429, 399-407 (2017).

2016

A. Vangone, J.P.G.L.M. Rodrigues, L.C. Xue, G.C.P. van Zundert, C. Geng, Z. Kurkcuoglu, M. Nellen, S. Narasimhan, E. Karaca, M. van Dijk, A.S.J. Melquiond, K.M. Visscher, M. Trellet, P.L. Kastritis and A.M.J.J. Bonvin. Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI Round 1. Proteins: Struc. Funct. & Bioinformatics, 85, 417-423 (2016). See also erratum: https://doi.org/10.1002/prot.25339
D. Walker, R. Grinter, I. Josts, K. Mosbahi, A. Roszak, R. Cogdell, A.M.J.J. Bonvin, J. Milner, S. Kelly, O. Byron and B. Smith. Structure of the bacterial plant-ferredoxin receptor FusA. Nature Communications, 7, 13228 (2016).
J. Felix, E. Kandiah, S. De Munck, Y. Bloch, G.C.P. van Zundert, K. Pauwels, A. Dansercoer, K. Novanska, R.J. Read, A.M.J.J. Bonvin, B. Vergauwen, K. Verstraete, I. Gutsche and S.N. Savvides. Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF to achieve immunomodulation. Nature Communications, 7, 13228 (2016).
Z. Kurkcuoglu and A.M.J.J. Bonvin. Science in the clouds: virtualizing HADDOCK, PowerFit and DisVis using INDIGO-DataCloud solutions. F1000Research, 5:874 (poster) (2016).
M. Trellet, J. Schaarschmidt, G.C.P. van Zundert, Z. Kurkcuoglu, A.S.J. Melquiond and A.M.J.J. Bonvin. Integrative modelling goes HPC/HTC. F1000Research, 5:2216 (poster) (2016).
A.D. Spiliotopoulos, P.L. Kastritis, A.S.J. Melquiond, A.M.J.J. Bonvin, G. Musco, W. Rocchia and A. Spitaleri. dMM-PBSA: a new HADDOCK scoring function for protein-peptide docking. Frontiers in Molecular Biosciences, 3:46 doi:10.3389/fmolb.2016.00046 (2016).
L.C. Xue, J.P.G.L.M. Rodrigues, P.L. Kastritis, A.M.J.J. Bonvin# and A. Vangone#. PRODIGY: a web server for predicting the binding affinity of protein-protein complexes. Bioinformatics, 32, 3676-3678 (2016).
R. Melo, R. Fieldhouse, A. Melo, J.D.G. Correia, M.D.S. Cordeiro, Z.H. Gumus, J. Costa, A.M.J.J. Bonvin and I.S. Moreira. A Machine-Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces. International Journal of Molecular Sciences, 17, 1215 (2016).
G.C.P van Zundert and A.M.J.J. Bonvin. Defining the limits and reliability of rigid-body fitting in cryo-EM maps using multi-scale image pyramids. J. Struct. Biol., 195, 252-258 (2016).
Y. Liu, J.P.G.L.M. Rodrigues, A.M.J.J. Bonvin, E.A. Zaal, C.R. Berkers, M. Heger, K. Gawarecka, E. Swiezewska, E. Breukink and M.R. Egmond. New Insight into the Catalytic Mechanism of Bacterial MraY from Enzyme Kinetics and Docking Studies. J. Biol. Chem., 291, 15057-15068 (2016).
C. Geng, A. Vangone and A.M.J.J. Bonvin. Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes. Protein Engineering, Design, and Selection, 29, 291-299 (2016).
L.C. Xue, J.P.G.L.M. Rodrigues, D. Dobbs, V. Honavarand A.M.J.J. Bonvin. Template-Based Protein-Protein Docking Exploiting Pairwise Interfacial Residue Restraints. Briefings in Bioinformatics, 18, 458-466 (2016).
M.F. Lensink, S. Velankar, A. Kryshtafovych, S. Huang, D. Schneidman-Duhovny, A. Sali, J. Segura, N.s Fernandez-Fuentes, S. Viswanath, R. Elber, S. Grudinin, P. Popov, E. Neveu, Hasup Lee, M. Baek, S. Park, L. Heo, G. Rie Lee, C. Seok, S. Qin, H. Zhou, D.W. Ritchie, B. Maigret, M. Devignes, A. Ghoorah, M. Torchala, R.A.G. Chaleil, P.A. Bates, E.t Ben-Zeev, M. Eisenstein, S.S. Negi, Z. Weng, T. Vreven, B.G. Pierce, T. M. Borrman, J. Yu, F. Ochsenbein, R. Guerois, A. Vangone, J.P.G.L.M. Rodrigues, G. van Zundert, M. Nellen, L. Xue, E. Karaca, A.S.J. Melquiond, K. Visscher, P.L. Kastritis, A.M.J.J. Bonvin, X. Xu, L. Qiu, C. Yan, J. Li, Z. Ma, J. Cheng, X. Zou, Y. Shen, L.X. Peterson, H. Kim, A. Roy, X. Han, J. Esquivel-Rodriguez, D. Kihara, X. Yu, N.J. Bruce, J.C. Fuller, R.C. Wade, I. Anishchenko, P.J. Kundrotas, I.A. Vakser, K. Imai, K.i Yamada, T. Oda, T. Nakamura, K. Tomii, C. Pallara, M. Romero-Durana, B. Jimenez-Garcia, I.H. Moal, J Fernandez-Recio, J. Young Joung, J. Yun Kim, K.g Joo, J. Lee, D. Kozakov, S. Vajda, S. Mottarella, D.R. Hall, D. Beglov, A. Mamonov, B. Xia, T. Bohnuud, C.A. Del Carpio, E. Ichiishi, N. Marze, D. Kuroda, S.S. Roy Burman, J.J. Gray, E. Chermak, L. Cavallo, R. Oliva, A. Tovchigrechko and S.J. Wodak. Prediction of homo- and hetero-protein complexes by ab-initio and template-based docking: a CASP-CAPRI experiment. Proteins: Struc. Funct. & Bioinformatics, 84, 323-348 (2016)
P. Sliz, P. Meyer, S. Socias, J. Key, E. Ransey, E.C. Tjon, A. Buschiazzo, M. Lei, C. Botka, J. Withrow, D.B. Neau, K. Rajashankar, K.S. Anderson, R. Baxter, S. Blacklow, T. Boggon, A.M.J.J. Bonvin, D. Borek, T. Brett, A. Caflisch, C. Chang, W. Chazin, K.D. Corbett, M. Cosgrove, S. Crosson, S. Dhe-Paganon, E. Di Cera, C. Drennan, M. Eck, B. Eichman, Q. Fan, A. Ferra-D Amara, J.S. Fraser, J.C. Fromme, K. Garcia, R. Gaudet, P. Gong, S. Harrison, E. Heldwein, Z. Jia, R. Keenan, A. Kruse, M. Kvansakul, J. McLellan, Y. Modis, Y. Nam, Zb. Otwinowski, E.F. Pai, P.J. Barbosa Pereira, C. Petosa, C.S. Raman, T. Rapoport, A. Roll-Mecak, M. Rosen, G. Rudenko, J. Schlessinger, T. Schwartz, Y. Shamoo, H. Sondermann, Y. Tao, N. Tolia, O.V. Tsodikov, K.D. Westover, H. Wu, I. Foster, F. Maia, T. Gonen, T. Kirchhausen, K. Diederichs and M. Crosas. Data publication with the structural biology data grid supports live analysis. Nature Communications, 7: 10882, 1-12 (2016).
S. Jung, J. Fischer, B. Spudy, K. Tim, F.D. Soennichsen, L. Xue, A.M.J.J. Bonvin, P. Goettig, V. Magdolen, U. Meyer-Hoffert, J. Grötzinger. The solution structure of the kallikrein-related peptidases inhibitor SPINK6. Biochemical and Biophysical Research Communications, 471, 103-108 (2016).
E. Deplazes, J. Davies, A.M.J.J. Bonvin, G.F. King and A.E. Mark. On the 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. J. Chem. Inf. and Model. 56, 127-138 (2016).
J.P.G.L.M. Rodrigues, A.S.J. Melquiond and A.M.J.J. Bonvin. 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, 160-167 (2016).
R. Zhang, T. Eckert, T. Lutteke, S. Hanstein, A. Scheidig, A.M.J.J. Bonvin, N.E. Nifantiev, T. Kozar, R. Schauer, M. Abdulaziz Enani and H.C. Siebert. Structure-function relationship of antimicrobial peptides and proteins in respect to contact-molecules on pathogen surfaces. Current Topics in Medicinal Chemistry. 16, 89-98 (2016).
G.C.P van Zundert, J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond, M. van Dijk, S.J. de Vries and A.M.J.J. Bonvin. The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes. J. Mol. Biol., 428, 720-725 (2016).

2015

M. Kalia, S. Willkomm, J.C. Claussen, T. Restle# and A.M.J.J. Bonvin#. Novel insights into guide RNA 5’-nucleoside/tide binding by human Argonaute 2. Int. J. Mol. Sci. 22, doi:10.3390/ijms17010022 (2015).
A.M.J.J. Bonvin and O. Keskin. Editorial overview: Protein-Protein Interactions. Curr. Opin. Struct. Biol. 35, vii-ix (2015). (free PDF download)
L.C. Xue, D. Dobbs. A.M.J.J. Bonvin and V. Honavar Computational Prediction of Protein Interfaces: A Review of Data Driven Methods. FEBS Letters, 589, 3516-3526 (2015).
F. Marino, M. Bern, G.P.M. Mommen, A.C. Leney, J.A.M. van Gaans-van den Brink, A.M.J.J. Bonvin, C. Becker, C.A.C.M. van Els and A.J.R. Heck. Extended O-GlcNAc on HLA Class-I-Bound Peptides. J. Am. Chem. Soc. 137, 10922-10925 (2015).
T Vreven+, I.H. Moal+, A. Vangone+, B.G. Pierce, P.L. Kastritis, M. Torchala, R. Chaleil, B. Jiménez-García, P.A. Bates#, Juan Fernandez-Recio#, A.M.J.J. Bonvin# and Z. Weng#. Updates to the integrated protein-protein interaction benchmarks: Docking benchmark version 5 and affinity benchmark version 2. J. Mol. Biol. 19, 3031-3041 (2015).
A Vangone and A.M.J.J. Bonvin. Contacts-based prediction of binding affinity in protein-protein complexes. eLife, 4, e07454 (2015).
M. Rad-Malekshahi, K. Visscher, J.P.G.L.M. Rodrigues, R. De Vries, W. Hennink, M. Baldus, A.M.J.J. Bonvin#, E. Mastrobattista# and M. Weingarth#. The supramolecular organization of a peptide-based nanocarrier at high molecular detail. J. Am. Chem. Soc. 137, 7775-7784 (2015).
G.C.P. van Zundert and A.M.J.J. Bonvin. DisVis: Quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes. Bioinformatics. 31, 3222-3224 (2015).
F. Psomopoulos, Af.M. Duarte, C. Blanchet, A.M.J.J. Bonvin, M. Corpas, A. Franc, R.C. Jimenez, J. Marco de Lucas, T. Nyrönen, G. Sipos and S.B. Suhr. Future opportunities and future trends for e-infrastructures and life sciences: going beyond grid to enable life science data analysis. Frontiers in Genetics. 6:197, doi:10.3389/fgene.2015.00197 (2015).
A. Sali, H.M. Berman, T. Schwede, J. Trewhella, G. Kleywegt, S.K. Burley, J. Markley, H. Nakamura, P. Adams, A.M.J.J. Bonvin, W. Chiu, M. Dal Peraro, F. Di Maio, T.E. Ferrin, K. Grünewald, A. Gutmanas, R. Henderson, G. Hummer, K. Iwasaki, G. Johnson, C.L. Lawson, J. Meiler, M.A. Marti-Renom, G.T. Montelione, M. Nilges, R. Nussinov, A. Patwardhan, J. Rappsilber, R.J. Read, H. Saibil, G.F. Schröder, C. Schwieters, C.A.M. Seidel, D. Svergun, M. Topf, E.L. Ulrich, S. Velankar, and J.D. Westbrook. Outcome of the First wwPDB Hybrid / Integrative Methods Task Force Workshop. Structure. 23, 1056-1067 (2015).
G. van der Schot and A.M.J.J. Bonvin. Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR. J. Biomol. NMR. 62, 497-502 (2015).
T. Sinnige, M. Weingarth, M. Daniëls, R. Boelens, A.M.J.J. Bonvin, K. Houben and M. Baldus. Conformational plasticity of the POTRA 5 domain in the outer membrane protein assembly factor BamA. Structure. 23, 1317-1324 (2015).
G.C.P. van Zundert and A.M.J.J. Bonvin. Fast and sensitive rigid-body fitting into cryo-EM density maps with PowerFit. AIMS Biophysics. 2, 73-87 (2015).
K.D. Brewer, T. Bacaj, A. Cavalli, C. Camilloni, J.D. Swarbrick, J. Liu, A. Zhou, P. Zhou, N. Barlow, J. Xu, A.B. Seven, E.A. Prinslow, R. Voleti, D. Haussinger, A.M.J.J. Bonvin, D.R. Tomchick, M. Vendruscolo, B. Graham, T.C. Sudhof, J. Rizo. Dynamic Synaptotagmin-1-SNARE Complex Binding Mode in Solution. Nature Struct. & Mol. Biol. 22, 555-564 (2015).
G.C.P. van Zundert, A.S.J. Melquiond and A.M.J.J. Bonvin. Integrative modeling of biomolecular complexes: HADDOCKing with Cryo-EM data. Structure. 23, 949-960 (2015).
M. Kaplan, A. Cukkemane, G.C.P. van Zundert, S. Narasimhan, G. Waksman, A.M.J.J. Bonvin, R. Fronzes, G.E. Folkers and M. Baldus. Probing a cell-embedded Megadalton protein complex by DNP-supported solid-state NMR. Nature Methods. 12, 649-652 (2015).
K.M. Visscher, P.L. Kastritis and A.M.J.J. Bonvin. Non-interacting surface solvation and dynamics in protein-protein interactions. Proteins: Struc. Funct. & Bioinformatics 83, 445-458 (2015).
M. Trellet, A.S.J. Melquiond and A.M.J.J. Bonvin. Information-driven modelling of protein-peptide complexes. Methods in Molecular Biology. Ed. Peng Zhou. Humana Press Inc. 221-239 (2015)
J.P.G.L.M Rodrigues, E. Karaca and A.M.J.J. Bonvin. Information-driven structural modelling of protein-protein interactions. Methods in Molecular Biology: Molecular Modelling of Proteins. Ed. Andreas Kokul. Humana Press Inc. 399-424 (2015).
W.F. Vranken, G.W. Vuister and A.M.J.J. Bonvin. NMR-based modelling and refinement of protein 3D structures. Methods in Molecular Biology: Molecular Modelling of Proteins. Ed. Andreas Kokul. Humana Press Inc. 351-380 (2015).

2014

F.M. Ferguson, D.M. Dias, J.P.G.L.M. Rodrigues, J. Wienk, R. Boelens, A.M.J.J. Bonvin, C. Abell, A. Cuilli. Binding Hotspots of BAZ2B Bromodomain: Histone Interaction Revealed by Solution NMR Driven Docking. Biochemistry. 53, 6706-6716 (2014).
T.A. Hopf#, C.P.I. Schärfe#, J.P.G.L.M. Rodrigues#, A.G. Green, O. Kohlbacher, C. Sander*, A.M.J.J. Bonvin* and D.S. Marks*. Sequence co-evolution gives 3D contacts and structures of protein complexes. eLife. 3 e03430 (2014)
M. Rey, V. Sarpe, K. Burns, J. Buse, Ch.A.H. Baker, M. van Dijk, L. Wordeman, A.M.J.J. Bonvin and D. Schriemer. Mass Spec Studio for Integrative Structural Biology. Structure. 22, 1538-1548 (2014).
P.L. Kastritis, J.P.G.L.M Rodrigues, G.E. Folkers, R. Boelens and A.M.J.J. Bonvin. Proteins feel more than they see: Fine-tuning of binding affinity by properties of the non-interacting surface. J. Mol. Biol. 426, 2632-2652 (2014).
J.P.G.L.M Rodrigues and A.M.J.J. Bonvin Integrative computational modeling of protein interactions. FEBS J., 281, 1988-2003 (2014).
P.L. Kastritis, J.P.G.L.M. Rodrigues and A.M.J.J. Bonvin HADDOCK2P2I: A robust biophysical model for predicting the binding affinity of protein-protein interaction inhibitors J. Chem. Info. Model. 54, 826-836 (2014).
H. van Ingen and A.M.J.J. Bonvin Information-driven modeling of large macromolecular assemblies using NMR data. J. Magn. Reson. 241, 103-114 (2014).
J. Snijder, R.J. Burnley, A. Wiegard, A.S.J. Melquiond, A.M.J.J. Bonvin, I.M. Axmann, A.J.R. Heck Insight into cyanobacterial circadian timing from structural details of the KaiB-KaiC interaction. Proc. Natl. Acad. Sci. USA. 111, 1379-1383 (2014).
G.C.P. van Zundert and A.M.J.J. Bonvin. Modeling protein-protein complexes using the HADDOCK webserver. Methods in Molecular Biology: Protein Structure Prediction. Ed. Daisuke Kihara. Humana Press Inc., 163-179 (2014).
M.F. Lensink, I.H. Moal, P.A. Bates, P.L. Kastritis, A.S.J. Melquiond, E. Karaca, C. Schmitz, M. van Dijk, A.M.J.J. Bonvin, M. Eisenstein, B. Jimenez-Garcia, S. Grosdidier, S.A Solernou, L. Perez-Cano, C. Pallara, J. Fernandez-Recio, J. Xu, P. Muthu, K. Praneeth Kilambi, J.J. Gray, S. Grudinin, G. Derevyanko, J.C. Mitchell, J. Wieting, E. Kanamori, Y. Tsuchiya, Y. Murakami, J. Sarmiento, D.M. Standley, M. Shirota, K. Kinoshita, H. Nakamura M. Chavent, D.W. Ritchie, H. Park, J. Ko, H. Lee, C. Seok, Y. Shen, D. Kozakov, S. Vajda, P. J. Kundrotas, I.A. Vakser, B.G. Pierce, H. Hwang, T. Vreven, Z. Weng, I. Buch, E. Farkash, H.J. Wolfson, M. Zacharias, S. Qin, H.-X. Zhou, S.-Y. Huang, X. Zou, J.A. Wojdyla, C. Kleanthous and S.J. Wodak. Blind Prediction of Interfacial Water Positions in CAPRI. Proteins: Struc. Funct. & Bioinformatics 82, 620-632 (2014).

2013

K.M. Varney#, A.M.J.J. Bonvin#, M. Pazgier#, J. Malin#, W. Yu#, E. Ateh, T. Oashi, J. Huang, W. Lu, M. Diepeveen-de Buin, J. Bryant, E. Breukink, A.D. MacKerell Jr. and E.P.H. de Leeuw Turning Defense into Offense: Development of Defensin Mimetics as Novel Antibiotics targeting Lipid II. PloS Pathogens, 9, e1003732. doi:10.1371/journal.ppat.1003732 (2013).
G. van der Schot, Z. Zhang, R. Vernon, Y. Shen, W.F. Vranken, D. Baker, A.M.J.J. Bonvin* and O.F. Lange* Improving 3D structure prediction from chemical shift data. J. Biomol. NMR., 57, 27-35 (2013).
A.M.J.J. Bonvin Coming to peace with protein complexes? 5th CAPRI evaluation meeting, April 17-19th 2013, Utrecht. Proteins: Struc. Funct. & Bioinformatics Editorial, CAPRI special issue. 81, 20173-2074 (2013).
J.P.G.L.M. Rodrigues, A.S.J. Melquiond, E. Karaca, M. Trellet, M. Van Dijk, G.C.P. Van Zundert, C. Schmitz, S.J. de Vries, A. Bordogna, L. Bonati, P.L. Kastritis and A.M.J.J. Bonvin Defining the limits of homology modelling in information-driven protein docking Proteins: Struc. Funct. & Bioinformatics, 81, 2119-2128 (2013).
R. Morretti et al. Community-wide Evaluation of Methods for Predicting the Effect of Mutations on Protein-Protein Interactions. Proteins: Struc. Funct. & Bioinformatics, 81, 1980-1987 (2013).
J. Janin and A.M.J.J. Bonvin Protein-Protein Interactions. Curr. Opin. Struct. Biol. Editorial, special issue on protein-protein interactions. 23, 859-861 (2013).
P.L. Kastritis and A.M.J.J. Bonvin Molecular origins of binding affinity: Seeking the Archimedean point. Curr. Opin. Struct. Biol., 23, 868-877 (2013).
D.M. Dias, J.P.G.L.M. Rodrigues, N.S. Domingues, A.M.J.J. Bonvin and M.C.A. Castro. Unveiling the Interaction of Vanadium Compounds with Human Serum Albumin using 1H STD NMR and Computational Docking Studies. Eur. J. Inorg. Chem., 26, 4619-4626 (2013).
E.A.W. van der Cruijsen, D. Nand, M. Weingarth, A, Prokofyev, S, Hornig, A.M.J.J. Bonvin, S. Becker, R.E. Hulse, E. Perozo, O. Pongs, M. Baldus. The importance of the lipid-pore loop interface for potassium channel structure and function. Proc Natl. Acad. Sci. USA, 110, 13008-13013. (2013).
M. van Dijk, K. Visscher, P.L. Kastritis and A.M.J.J. Bonvin. Solvated protein-DNA docking using HADDOCK. J. Biomol. NMR, 56, 51-63 (2013).
E. Karaca and A.M.J.J. Bonvin. On the usefulness of Ion Mobility Mass Spectrometry and SAXS data in scoring docking decoys. Acta Cryst. D., D69, 683-694 (2013).
M. Weingarth, A. Prokofyev, E. van der Cruijsen, D. Nand, A.M.J.J. Bonvin, O. Pongs and M. Baldus Structural determinants and functional aspects of specific lipid binding to potassium channels. J. Am. Chem. Soc., 35, 3983-3988 (2013).
S. Alex, K. Lange, T. Amolo, J.S. Grinstead, E. Szalowska, A. Koppen, K. Mudde, D. Haenen, S. Al-Lahham, H. Roelofsen, R. Houtman, B. van der Burg, A.M.J.J. Bonvin, E. Kalkhoven, M. Muller, G. Hooiveld and S. Kersten. Short chain fatty acids stimulate Angptl4 synthesis in human colonocytes by selective PPAR modulation. Mol. Cell. Biol., 33, 1303-1316 (2013).
D.L. Hulsik, Y.Y. Liu, N.M. Strokappe, S. Battella, M. El Khattabi, L.E. McCoy, A. Hinz, M. Hock, A.M.J.J. Bonvin, J.P.M. Langedijk, D. Davis, A. Forsman Quinley, M. Aasa-Chapman, R.A. Weiss, C.T. Verrips, W. Weissenhorn and L. Rutten A gp41 MPER-specific Llama VHH Requires a Hydrophobic CDR3 for Neutralization but not for Antigen Recognition. PloS Pathogens, 9, e1003202 (2013).
M. Trellet, A.S.J. Melquiond and A.M.J.J. Bonvin. A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking PLoS ONE, 8(3) e58769 (2013). –> ERRATUM
R. Dagil, C O’Shea, A. Nykaer, A.M.J.J. Bonvin and B.B. Kragelund Gentamicin Binds to Megalin as a Competitive Inhibitor and Utilizes the Common Ligand Binding Motif of Complement Type Repeats. J. Biol. Chem, 288, 4424-4435 (2013).
E. Karaca and A.M.J.J. Bonvin Advances in integrated modelling of biomolecular complexes. Methods, 59, 372-381 (2013).
P.L. Kastritis and A.M.J.J. Bonvin On the binding affinity of macromolecular interactions: daring to ask why proteins interact J. R. Soc. Interface, 10, doi: 10.1098/rsif.2012.0835 (2013).
A.M.J.J. Bonvin, M. van Dijk, E. Karaca, P.L. Kastritis, A.S.J. Melquiond, C. Schmitz and S.J. de Vries HADDOCK In Encyclopedia of Biophysics, Ed. G.C.K. Roberts, Springer-Verlag Berlin Heidelberg (2013).
P.L. Kastritis, K.M. Visscher, A.D.J. van Dijk and A.M.J.J. Bonvin Solvated docking using Kyte-Doolittle-based water propensities. Proteins: Struc. Funct. & Bioinformatic., 81, 510-518 (2013).

2012

S. Gradmann, C. Ader, I. Heinrich, D. Nand, M. Dittmann, A. Cukkemane, M. van Dijk, A.M.J.J. Bonvin, M. Engelhard and M. Baldus Rapid Prediction of multi-dimensional NMR data sets. J. Biomol. NMR, 54, 377-387 (2012).
J. Hennig, S. de Vries, K.D.M. Hennig, L. Randles, K.J. Walters, M. Sunnerhagen and A.M.J.J. Bonvin MTMDAT-HADDOCK: High-throughput, protein complex structure modeling based on limited proteolysis and mass spectrometry. BMC Struc. Biol., 12, 29 (2012).
S.J.L. van Wijk, A.S.J. Melquiond, S.J. de Vries, H.Th.M Timmers and A.M.J.J. Bonvin Dynamic control of selectivity in E2-E3 interactions via a salt-bridge network revealed by an ASP to GLU substitution. PLoS Comp. Biol., 8(11), e1002754 (2012).
T.A. Wassenaar, M. van Dijk, N. Loureiro-Ferreira, G. van der Schot, S.J. de Vries, C. Schmitz, J. van der Zwan, R. Boelens, A. Giachetti, L. Ferella, A. Rosato, I. Bertini, T. Herrmann, H.R.A. Jonker, A. Bagaria, V. Jaravine, P. Guntert, H. Schwalbe, W.F. Vranken, J.F. Doreleijers, G. Vriend, G.W. Vuister, D. Franke, A. Kikhney, D.I. Svergun, R. Fogh, J. Ionides, E.D. Laue, C. Spronk, S. Jurka, M. Verlato, S. Badoer, S. Dal Pra, M. Mazzucato, E. Frizziero and A.M.J.J. Bonvin WeNMR: Structural Biology on the Grid. J. Grid. Comp., 10, 743-767 (2012).
T.A. Wassenaar, S.J.L. de Vries, H. Bekker and A.M.J.J. Bonvin SQUEEZE-E: The optimal solution for molecular simulations with periodic boundary conditions. J. Chem. Theo. Comput., 8, 3618-3627 (2012).
M. van Dijk, T.A. Wassenaar and A.M.J.J. Bonvin A flexible, grid-enabled web portal for GROMACS molecular dynamics simulations J. Chem. Theo. Comput., 8, 3463-3472 (2012).
P.L. Kastritis and A.M.J.J. Bonvin Predicting and Dissecting High-order Molecular Complexity by Information-driven Biomolecular Docking In: Antimicrobial Drug Discovery. Emerging Strategies Adv. Mol. Cell. Microbiol., Eds G. Tegos and E. Mylokanis, CABI, 22, 232-246 (2012).
M. Weingarth, C. Ader, A.S.J. Melquiond, D. Nand, O. Pongs, S. Becker, A.M.J.J. Bonvin and M. Baldus. Supramolecular structure of membrane-associated polypeptides by combining solid-state NMR and Molecular Dynamics simulations. Biophys. J., 103, 29-37 (2012).
J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond and A.M.J.J. Bonvin Clustering biomolecular complexes by residue contacts similarity. Proteins: Struc. Funct. & Bioinformatic, 80, 1810-1817 (2012).
C. Schmitz, A.S.J. Melquiond, S.J. de Vries, E. Karaca, M. van Dijk, P.L. Kastritis and A.M.J.J. Bonvin Protein-protein docking with HADDOCK In: NMR in Mechanistic Systems Biology. Ed. I. Bertini, K.S. McGreevy and G. Parigi, Wiley-Blackwell, 512-535.
A. Rosato, J. M. Aramini, C. Arrowsmith, A. Bagaria, D. Baker, A. Cavalli, J.F. Doreleijers, A. Eletsky, A. Giachetti, P. Guerry, A. Gutmanas, P. Guntert, Y. He, T. Herrmann, Y.J. Huang, V. Jaravine, H.R.A. Jonker, M.A. Kennedy, O.F. Lange, G. Liu, T.E. Malliavin, R. Mani, B. Mao, G.T. Montelione, M. Nilges, P. Rossi, G. van der Schot, H. Schwalbe, T.A. Szyperski, M. Vendruscolo, R. Vernon, W.F. Vranken, S.J. de Vries, G.W. Vuister, B. Wu, Y. Yang and A.M.J.J. Bonvin Blind testing of routine, fully automated determination of protein structures from NMR data. Structure, 20, 227-236 (2012).
P.L. Kastritis, A.D.J. van Dijk and A.M.J.J. Bonvin Explicit Treatment of Water Molecules in Data-Driven Protein-Protein Docking: The Solvated HADDOCKing Approach Methods in Molecular Biology 819, Part 5, 355-374 (2012)
A.S.J. Melquiond, E. Karaca, P.L. Kastritis and A.M.J.J. Bonvin Next challenges in protein-protein docking: From proteome to interactome and beyond. WIREs Computational Molecular Science, 2, 642-651 (2012).
T.A. Wassenaar, M. van Dijk, N. Loureiro-Ferreira, G. van der Schot, S.J. de Vries, C. Schmitz, J. van der Zwan, R. Boelens, A. Giachetti, L. Ferella, A. Rosato, I. Bertini, T. Herrmann, H.R.A. Jonker, A. Bagaria, V. Jaravine, P. Guntert, H. Schwalbe, W.F. Vranken, J.F. Doreleijers, G. Vriend, G.W. Vuister, D. Franke, A. Kikhney, D.I. Svergun, R. Fogh, J. Ionides, E.D. Laue, C. Spronk, M. Verlato, S. Badoer, S. Dal Pra, M. Mazzucato, E. Frizziero and A.M.J.J. Bonvin WeNMR: Structural Biology on the Grid. In: IWSG-Life 2011: Science Gateways for Life Sciences 2011. Proceedings of the 3rd International Workshop on Science Gateways for Life Sciences London, United Kingdom. June 8-10, 2011. Eds G. Terstyanszky and T. Kiss. urn:nbn:de:0074-819-5

2011

S.J Fleishman, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology J. Mol. Biol., 414, 289-302 (2011).
A.M. Wu, T, Singh, J.-H, Liu, S, Andre, M, Lensch, H-C, Siebert, M, Krzeminski, A.M.J.J. Bonvin, H, Kaltner, J,H. Wu and H.-J. Gabius Adhesion/Growth-Regulatory Galectins: Insights into Their Ligand Selectivity Using Natural Glycoproteins and Glycotopes In: The Molecular Immunology of Complex Carbohydrates-3, Advances in Experimental Medicine and Biology. A.M. Wu (ed.). Springer Science+Business Media, LLC. pp. 117-141 (2011)
C. Schmitz and A.M.J.J. Bonvin Protein-Protein HADDocking using exclusively Pseudocontact Shifts. J. Biomol. NMR, 50, 263-266 (2011).
D. Stratman, R. Boelens and A.M.J.J. Bonvin Quantitative use of chemical shifts for the modelling of protein complexes. Proteins: Struc. Funct. & Bioinformatic, 79, 2662-2670 (2011).
E. Escobar-Cabrera, Okon, D.K.W. Lau, C.F. Dart, A.M.J.J. Bonvin and L.P. McIntosh Characterizing the N- and C-terminal SUMO interacting motifs of the scaffold protein DAXX. J. Biol. Chem., 286, 19816-19829 (2011).
Y.C. Fiamegos, P.L. Kastritis, V. Exarchou, H. Han, A.M.J.J. Bonvin, J. Vervoort, K. Lewis, M.R. Hamblin and G.P. Tegos Antimicrobial and efflux pump inhibitory activity of caffeoylquinic acids from Artemisia absinthium against Gram-positive pathogenic bacteria. PlosONE, 6 e18127 (2011).
S.J. de Vries and A.M.J.J. Bonvin CPORT: a Consensus Interface Predictor and its Performance in Prediction-driven Docking with HADDOCK. PlosONE, 6 e17695 (2011).
C. Koehler, L. Carlier, D. Veggi, E. Balducci, F. Di Marcello, M. Ferrer-Navarro, M. Pizza, X. Daura, M. Soriani, R. Boelens and A.M.J.J. Bonvin Structural and biochemical characterization of Nar E, an iron containing ADP-ribosyltransferase from Neisseria meningitides. J. Biol. Chem., 286, 14842-14851 (2011).
E. Karaca and A.M.J.J. Bonvin A multi-domain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes. Structure, 19 555-565(2011).
P.L. Kastritis, I.H. Moal, H. Hwang, Z. Weng, P.A. Bates, A.M.J.J. Bonvin and J. Janin A structure-based benchmark for protein-protein binding affinity. Prot. Sci., 20, 482-41 (2011).
A. Neumoin, A. Leonchiks, P. Petit, L. Vuillard, M. Pizza, M. Soriani, R. Boelens and A.M.J.J. Bonvin 1H, 13C and 15N assignment of the GNA1946 outer membrane lipoprotein from Neisseria meningitidis. Biomol. NMR. Assign., DOI 10.1007/s12104-010-9285-y.
M. Krzeminski, T. Singh, S. Andre, M. Lensch, A.M. Wu, A.M.J.J. Bonvin and H.-J. Gabius 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, 1810, 150-161 (2011).
L. Carlier, C. Koehler, D. Veggi, M. Pizza, M. Soriani, R. Boelens and A.M.J.J. Bonvin NMR resonance assignments of NarE, a putative ADP-ribosylating toxin from Neisseria meningitides. Biomol. NMR. Assign., DOI 10.1007/s12104-010-9261-6.

2010

G. Nicastro, S. Todi, E. Karaca, A.M.J.J. Bonvin, H. Paulson, A. Pastore Understanding the polyUb binding and cleavage properties of ataxin-3. PlosONE, 5, e12430 (2010).
S.J. de Vries, A.S.J. Melquiond, P.L. Kastritis, E. Karaca, A. Bordogna, M. van Dijk, J.P.G.L.M. Rodrigues and A.M.J.J. Bonvin Strengths and weaknesses of data-driven docking in CAPRI Proteins: Struc. Funct. & Bioinformatic, 78, 3242-3249 (2010).
T. Schneider, Th. Kruse, R. Wimmer, I. Wiedemann, V. Sass, U. Pag, A. Jansen, A.K. Nielsen, P.H. Mygind, D.S. Raventos, S. Neve, B. Ravn, A.M.J.J. Bonvin, L. De Maria, L. Kamenova, H.-G. Sahl and H.-H. Kristensen Plectasin, a fungal defensin antibiotic peptide, targets the bacterial cell wall precursor Lipid II. Science, 328, 1168-1172 (2010). Download the final author version here.
A.S.J. Melquiond and A.M.J.J. Bonvin Data-driven docking: using external information to spark the biomolecular rendez-vous. In: Protein-protein complexes: analysis, modelling and drug design. Edited by M. Zacharrias, Imperial College Press, 2010. p 183-209.
P. Kastritis and A.M.J.J. Bonvin Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark. J. Proteome Research, 9, 2216-2225 (2010). See also the published correction
E. Karaca, A.S.J. Melquiond, S.J. de Vries, P.L. Kastritis and A.M.J.J. Bonvin Building macromolecular assemblies by information-driven docking: Introducing the HADDOCK multi-body docking server. Mol. Cell. Proteomics, 9, 1784-1794 (2010). Download the final author version here.
M. van Dijk and A.M.J.J. Bonvin Pushing the limits of what is achievable in protein-DNA docking. Benchmarking HADDOCK’s performance. Nucl. Acids Res., 38, 5634-5647 (2010).
A.M.J.J. Bonvin, A. Rosato and T.A. Wassenaar The eNMR platform for structural biology. J. Struct. Funct. Genomics, 11, 1-8 (2010).
S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, 5, 883-897 (2010).
M. Krzeminski, K. Loth, R. Boelens and A.M.J.J. Bonvin SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes. BMC Bioinformatics, 11, 51 (2010).
M. Kobayashi, E. AB, A.M.J.J. Bonvin and G. Siegal Structure of the DNA bound BRCT region from human Replication Factor C p140 and model of the protein-DNA complex. J. Biol. Chem., 285, 10087-10097 (2010).

2009

A. Rosato, A. Bagaria, Da. Baker, B. Bardiaux, A. Cavalli, J.F. Doreleijers, A. Giachetti, P. Guerry, P. Güntert, T. Herrmann, Y.J. Huang, H.R.A. Jonker, B. Mao, T.E. Malliavin, G.T. Montelione, M. Nilges, S. Raman, G. van der Schot, W.F. Vranken, G.W. Vuister and A.M.J.J. Bonvin CASD-NMR: Critical Assessment of Automated Structure Determination by NMR. Nature Methods, 6, 625-626 (2009).
S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin The Prediction of Macromolecular Complexes by Docking. In: Prediction of Protein Structures, Functions, and Interactions (ed J. M. Bujnicki), John Wiley & Sons, Ltd, Chichester, UK (2009).
D. Eggink, J.P.M. Langedijk, A.M.J.J. Bonvin, Y. Deng, M. Lu, B. Berkhout and R.W. Sanders Detailed mechanistic insights into HIV-1 sensitivity to three generations fusion inhibitors. J. Biol. Chem., 284, 26941-26950 (2009).
S.J.L. van Wijk, S.J. de Vries, P. Kemmeren, A. Huang, R. Boelens, A.M.J.J. Bonvin and H.Th. M. Timmers A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system. Mol. Sys. Biol., 5, 295 (2009).
J. Romanuka, G.E. Folkers, N. Biris, E. Tishchenko, H. Wienk, A.M.J.J. Bonvin, R. Kaptein and R. Boelens Specificity and Affinity of Lac Repressor for the Auxiliary Operators O2 and O3 Are Explained by the Structures of Their Protein-DNA Complexes. J. Mol. Biol., 390, 478-489 (2009).
M. van Dijk and A.M.J.J. Bonvin 3D-DART: a DNA structure modelling server. Nucl. Acids Res., 37, W235-W239 (2009).
L. Rutten, J.-P.B.A. Mannie, C.M. Stead, C.R.H. Raetz, C.M. Reynolds, A.M.J.J. Bonvin, J. Tommassen, M.R. Egmond, M.S. Trent and Piet Gros Active site architecture and catalytic mechanism of the lipid A deacylase LpxR of Salmonella typhimurium. Proc. Natl. Acad. Sci., 106, 1960-1964 (2009).
T. Stockner, S. de Vries, A.M.J.J. Bonvin, G. Ecker, P. Chiba Data-driven homology modelling of P-glycoprotein in the ATP-bound state indicates flexibility of the transmembrane domains. FEBS J., 276, 964-972 (2009).
S. Jung, A.J. Dingley, R. Augustin, F. Anton-Erxleben, M. Stanisak, C. Gelhaus, T. Gutsmann, M.U. Hammer, R. Podschun, A.M.J.J. Bonvin, M. Leippe, T.C.G. Bosch and J. Groetzinger Hydramacin-1: Structure and antibacterial activity of a protein from the basal metazoan Hydra J. Biol. Chem., 284, 1896-1905 (2009).
K. Repanas, G. Fuentes, S.X. Cohen, A.M.J.J. Bonvin and Anastassis Perrakis Insights into the DNA cleavage mechanism of human LINE-1 retrotransposon endonuclease. Proteins: Struc. Funct. & Bioinformatic, 74, 917-928 (2009).
M. Krzeminski, G. Fuentes, R. Boelens and A.M.J.J. Bonvin MINOES: a new approach to select a representative ensemble of structures in NMR studies of (partially) unfolded states. Application to d25-PYP. Proteins: Struc. Funct. & Bioinformatic, 74, 894-905 (2009).

2008

C.J. Arnusch, A.M.J.J. Bonvin, A.M. Verel, W.T.M. Jansen, R.M.J. Liskamp, B. de Kruijff, R.J. Pieters, E. Breukink Vancomycin-nisin(1-12) conjugate restores activity against vancomycin resistant enterococci (VRE) Biochemistry, 47, 12661-12663 (2008).
R.W. Sanders, S.-T. H. Hsu, E. van Anken, M. Liscaljet, M. Dankers, I. Bontjer, A. Land, I. Braakman, A.M.J.J. Bonvin and B. Berkhout Evolution Rescues Folding of HIV-1 Envelope Glycoprotein GP120 Lacking a Conserved Disulfide Bond Mol. Biol. Cell, 19, 4707-4716 (2008).
M. van Dijk and A.M.J.J. Bonvin A protein-DNA docking benchmark. Nucl. Acids Res. (2008), 36, e88, doi: 10.1093/nar/gkn386.
S. de Vries and A.M.J.J. Bonvin How proteins get in touch: Interface prediction in the study of biomolecular complexes. Curr. Pept. and Prot. Research, 9, 394-406 (2008).
F. Correa, R. Kopke Salinas, A.M.J.J. Bonvin and C.S. Farah Deciphering the role of the electrostatic interactions in the a-Tropomyosin head-to-tail complex. Proteins: Struc. Funct. & Bioinformatic, 73, 902-917 (2008).
G. Fuentes, A.D.J. van Dijk and A.M.J.J. Bonvin NMR-based modelling and refinement of protein 3D structures and their complexes. In: Methods in Molecular Biology 443: Molecular Modelling of Proteins. A. Kukol Ed., Humana Press, pp. 175-186 (2008).

2007

I. Gelis, A. M. J. J. Bonvin, D. Keramisanou, M. Koukaki, G. Gouridis, S. Karamanou, A. Economou and C.G. Kalodimos Structural basis for signal sequence recognition by the translocase motor SecA determined by NMR Cell, 131, 756-769 (2007).
S.J. de Vries, A.D.J. van Dijk, M. Krzeminski, M. van Dijk, A. Thureau, V. Hsu, T. Wassenaar and A. M. J. J. Bonvin HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets. Proteins: Struc. Funct. & Bioinformatic 69, 726-733 (2007).
S. Tomaselli, L. Ragona, L. Zetta, M. Assfalg, P. Ferranti, R. Longhi, A. M. J. J. Bonvin and H. Molinari. NMR-based modeling and binding studies of a ternary complex between chicken liver bile acid binding protein and bile acids. Proteins: Struc. Funct. & Bioinformatic, 69 177-191 (2007).
A.D.J. van Dijk, S. Ciofo-Bafoni, L. Banci, I. Bertini, R. Boelens and A. M. J. J. Bonvin. Modelling protein-protein complexes involved in the cytochrome c oxidase copper-delivery pathway. J. Proteome Research, 6 1530-1539 (2007).
E.H. Jeninga, O. van Beekum, A.D.J. van Dijk, N. Hamers, B.I. Hendriks-Stegeman, A. M. J. J. Bonvin, R. Berger and E. Kalkhoven Impaired Peroxisome Proliferator-Activated Receptor gamma Function through Mutation of a Conserved Salt Bridge (R425C) in Familial Partial Lipodystrophy. Molecular Endocrinology, 21 1049-1065 (2007).
A. M. Wu, T. Singh, J.-H. Liu, M. Krzeminski, R. Russwurm, H.-C. Siebert, A. M. J. J. Bonvin, Sabine Andre, H.-J. Gabius 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 (2007).

2006

A.D.J. van Dijk and A.M.J.J. Bonvin Solvated docking: introducing water into the modelling of biomolecular complexes. Bioinformatics, 22 2340-2347 (2006).
G.A. Jensen, O.M. Andersen, A.M.J.J. Bonvin, I. Bjerrum-Bohr, M. Etzerodt, H.C. Thogersen, F.M. Poulsen1 and B.B. Kragelund Binding Site Structure of One LRP/RAP Complex -Implications for a Common Ligand/Receptor Binding Motif. J. Mol. Biol., 362 700-716 (2006).
S.J. de Vries and A.M.J.J. Bonvin Intramolecular surface contacts contain information about protein-protein interface regions. Bioinformatics, 22 2094-2098 (2006).
M. van Dijk, A.D.J. van Dijk, V. Hsu, R. Boelens and A.M.J.J. Bonvin Information-driven Protein-DNA Docking using HADDOCK: it is a matter of flexibility. Nucl. Acids Res., 34 3317-3325 (2006).
J.P. Langedijk, G. Fuentes, R. Boshuizen and A.M.J.J. Bonvin Two-rung model of a left-handed beta-helix for prions explains species barrier and strain variation in TSEs. J. Mol. Biol., 360 907-920 (2006).
L. Rutten, J. Geurtsen, W. Lambert, J.J. Smolenaers, A.M.J.J. Bonvin, A. de Haan, P. van der Ley, M.R. Egmond, P. Gros and J. Tommassen. Crystal structure and catalytic mechanism of the LPS 3-O-deacylase PagL from Pseudomonas aeruginosa. Proc. Natl. Acad. Sci., 103 7071-7076-244 (2006).
N. Sibille, A. Favier, A.I. Azuaga, G. Ganshaw, R. Bott, A.M.J.J. Bonvin, R. Boelens & N.A.J. van Nuland Comparative NMR study on the impact of point mutations on protein stability of Pseudomonas mendocina lipase. Prot. Sci., 15 1915-1927 (2006).
E. AB, D.J.R. Pugh, R. Kaptein, R. Boelens and A.M.J.J. Bonvin Direct Use of Unassigned Resonances in NMR Structure Calculations with Proxy Residues J. Am. Chem. Soc., 128, 7566-7571 (2006).
A.D.J. van Dijk, R. Kaptein, R. Boelens and A.M.J.J. Bonvin Combining NMR relaxation with chemical shift perturbation data to drive protein-protein docking J. Biomol. NMR, 34, 237-244 (2006).
F.J. Fuchs, A.M.J.J. Bonvin^*, B. Bochicchio, A. Pepe, A.J.P. Alix and A.M. Tamburro Kinetics and thermodynamics of type VIII beta-turn formation: a CD, NMR and microsecond explicit molecular dynamics study of the GDNP tetrapeptide. Biophys. J., 90, 2745-2759 (2006).
A.M.J.J. Bonvin Flexible protein-protein docking. Curr. Opin. Struct. Biol., 16, 194-200 (2006).
M.B. Kamphuis, A.M.J.J. Bonvin, M.C. Monti, M. Lemonnier, A. Munoz-Gomez, R.H.H. van den Heuvel, R. Diaz-Orejas and R. Boelens Model for RNA Binding and the Catalytic Site of the RNase Kid of the Bacterial parD Toxin-Antitoxin System. J. Mol. Biol., 357, 115-126 (2006).
S.J. de Vries, A.D.J. van Dijk and A.M.J.J. Bonvin WHISCY: WHat Information does Surface Conservation Yield? Application to data-driven docking. Proteins: Struc. Funct. & Bioinformatics, 63, 479-489 (2006).
S. Tomaselli, V. Esposito, P. Vangone, N.A.J. van Nuland, A.M.J.J. Bonvin, R. Guerrini, T. Tancredi, P.A. Temussi and D. Picone. The alpha-to-beta conformational transition of Alzheimer’s Abeta-(1-42) peptide in aqueous media is reversible: a step by step conformational analysis suggests the location of beta conformation seeding. Chem. Bio. Chem., 7, 257-267 (2006).
J.S. Grinstead, S.-T D. Hsu, W. Laan, A.M.J.J. Bonvin, K.J. Hellingwerf, R. Boelens and R. Kaptein The solution structure of the AppA BLUF domain: Insight into the mechanism of light-induced signaling. Chem. Bio. Chem, 7, 187-193 (2006).

2005

G. Fuentes, A.J. Nederveen, R. Kaptein, R. Boelens and A.M.J.J. Bonvin Describing partially unfolded states from sparse NMR data. J. Biomol. NMR, 33 175-186 (2005).
A.M.J.J. Bonvin, R. Boelens and R. Kaptein NMR analysis of protein interactions Curr. Opin. Chem. Biol., 9, 501-508 (2005).
R.K. Salinas, G.E. Folkers, A.M.J.J. Bonvin, D. Das, R. Boelens and R. Kaptein. Altered specificity in DNA binding by the lac repressor: a mutant lac headpiece that minics the gal repressor. Chem. Bio. Chem., 9, 1628-1637 (2005).
A.D.J. van Dijk, S.J. de Vries, C. Dominguez, H. Chen, H.-X. Zhou and A.M.J.J. Bonvin Data-driven docking: HADDOCKs adventures in CAPRI. Proteins: Struc. Funct. & Bioinformatics, 60, 232-238 (2005).
A.D.J. van Dijk, D. Fushman and A.M.J.J. Bonvin 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: Struc. Funct. & Bioinformatics, 60 367-381(2005).
A.J. Nederveen and A.M.J.J. Bonvin NMR relaxation and internal dynamics of ubiquitin from a 0.2 microsecond MD simulation. J. Chem. Theo. Comput., 1, 363-374 (2005).
K.F. Lin, Y.N. Liu, S.-T. D. Hsu, D. Samuel, C.-H. Cheng, A.M.J.J. Bonvin and P.-C. Lyu Characterization and structural analyses of nsLTP1 from mung bean. Biochemistry, 44, 5703-5712 (2005).
A.J. Nederveen, J.F. Doreleijers, W. Vranken, Z. Miller, C.A.E.M. Spronk, S.B. Nabuurs, P. Guntert, M. Livny, J.L. Markley, M. Nilges, E.L. Ulrich, R. Kaptein and A.M.J.J. Bonvin RECOORD: a REcalculated COORdinates Database of 500+ proteins from the PDB using restraints from the BioMagResBank Proteins: Struc. Funct. & Bioinformatics, 59, 662-672 (2005).
J.F. Doreleijers, A.J. Nederveen, W. Vranken, J. Lin, A.M.J.J. Bonvin, R. Kaptein, J.L. Markley and E.L. Ulrich BioMagResBank databases DOCR and FRED with converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. J. Biomol. NMR, 32, 1-12 (2005).
A.N. Volkov, D. Ferrari, J.A.R. Worrall, A.M.J.J. Bonvin and M. Ubbink 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 (2005).
A.D.J. van Dijk, R. Boelens and A.M.J.J. Bonvin Data-driven docking for the study of biomolecular complexes. FEBS Journal, 272, 293-312 (2005).
S.-T. D. Hsu, C. Peter, W.F. van Gunsteren and A.M.J.J. Bonvin Entropy calculation of HIV-1 Env gp120, its receptor CD4 and their complex: an analysis of entropy changes upon complexation. Biophys. J., 88, 15-24 (2005).

2004

K. Houben, C. Dominguez, F.M.A. van Schaik, H.Th.M. Timmers, A.M.J.J. Bonvin and R. Boelens Solution structure of the ubiquitin conjugating enzyme UbcH5B. J. Mol. Biol., 344, 513-526 (2004).
S.-T. D. Hsu, E. Breukink, E. Tischenko, M.A.G. Lutters, B. de Kruijff, R. Kaptein, A.M.J.J. Bonvin and N.A.J. van Nuland The nisin-lipid II complex reveals a pyrophosphate cage that provides a blueprint for novel antibiotics Nature Struc. & Mol. Biol., 11, 963-967 (2004).
A.G. Tzakos, P. Fuchs, N.A.J. van Nuland, A. Troganis, T. Tselios, S. Deraos, J. Matsoukas, I.P. Gerothanassis and A.M.J.J. Bonvin NMR and MD Studies of an Autoimmune MBP Peptide and its Antagonist. Structural Implications for the MHC II (I-Au) Peptide Complex through Docking Calculations. Eur. J. Biochem.,271, 3399-3413 (2004).
C.G. Kalodimos, N. Biris,A.M.J.J. Bonvin, M.M. Levandoski, M. Guennuegues, R. Boelens, R. Kaptein Structure and flexibility adaptation between nonspecific and specific protein-DNA complexes. Science, 205 386-389 (2004).
S.B. Nabuurs, A.J. Nederveen, W. Wranken, J.F. Doreleijers, A.M.J.J. Bonvin, G.W.Vuister, G. Vriend and C.A.E.M. Spronk DRESS, a Database of REfined Solution nmr Structures. Proteins: Struc. Funct. & Bioinformatics, 55 483-486 (2004).
S.-T.D. Hsu and A.M.J.J. Bonvin Atomic insight into the CD4 binding-induced conformational changes in HIV-1 gp120. Proteins: Struc. Funct. & Bioinformatics, 55 582-593 (2004).
C. Dominguez, A.M.J.J. Bonvin, G.S. Winkler, F.M.A. van Schaik, H.Th.M. Timmers and R.Boelens Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis and docking approaches. Structure, 12 633-644 (2004).
F. Arnesano, L. Banci, I. Bertini and A.M.J.J. Bonvin A docking approach to the study of copper trafficking proteins: interaction between metallochaperones and soluble domains of copper ATPases. Structure, 12 669-676 (2004).
A. van Drogen-Petit, C. Zwahlen, M. Peter and A.M.J.J. Bonvin Insight into molecular interactions between two PB1 domains. J. Mol. Biol., 336/5 1195-1210 (2004).

2003

P. Fuchs, A.M.J.J. Bonvin, A. Pepe, A.J.P. Alix and A.M. Tamburro Spectroscopic and theoretical characterisation of the type VIII beta-turn. Study of the tetrapeptide GDNP. In: Elastin 2002, edited by A.M. Tamburro and A. Pepe. EditricErmes, Potenza, Italy, pp. 81-88 (2003).
L.M.I. Koharudin, A.M.J.J. Bonvin, R. Kaptein and R. Boelens Use of very long range NOEs in a fully deuterated protein: an approach for rapid protein fold determination. J. Magn. Reson., 163, 228-235 (2003).
C.J. Oomen, P. Hoogerhout, A.M.J.J. Bonvin, B. Kuipers, H. Brugghe, H. Timmermans, S.R. Haseley, L. van Alphen and P. Gros Immunogenicity of peptide-vaccine candidates predicted by molecular dynamics simulations. J. Mol. Biol., 328, 1083-1089 (2003).
S.-T. D. Hsu, E. Breukink, G. Bierbaum, H.-G. Sahl, D. de Kruijff, R. Kaptein, N.A.J. van Nuland and A.M.J.J. Bonvin NMR study of mersacidin and lipid II interaction in dodecylphosphocholine micelles. Conformational changes are a key to antimicrobial activity. J. Biol. Chem., 278, 13110-13117 (2003).
T. Stockner, H. Sterk, R. Kaptein and A.M.J.J. Bonvin Molecular dynamics simulations of a molecular switch in the glucocorticoid receptor. J. Mol. Biol., 328, 325-334 (2003).
A.G. Tzakos, A.M.J.J. Bonvin, A. Troganis, P. Cordopatis, M.L. Amzel, I.P. Gerothanassis and N.A.J. van Nuland On the molecular basis of the recognition of angiotensin II (AII): NMR structure of AII in solution versus the X-ray structure of AII bound to the monoclonal antibody Fab131. Eur. J. Biochem., 270, 849-860 (2003).
C. Dominguez, R. Boelens and A.M.J.J. Bonvin HADDOCK: A protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc., 125, 1731-1737 (2003).
J. Linge, M.A. Williams, C.A.E.M. Spronk, A.M.J.J. Bonvin^* and M. Nilges^* Refinement of protein structures in explicit solvent. PROTEINS: Struct. Funct. & Genetics 50, 496-506 (2003).
C.A.E.M. Spronk, S.B. Nabuurs, A.M.J.J. Bonvin, E. Krieger, G.W. Vuister and G. Vriend The precision of NMR structure ensembles revisited. J. Biomol. NMR 25, 225-234 (2003).

2002

C.G. Kalodimos, A.M.J.J. Bonvin, R.K. Salinas, R. Wechselberger, R. Boelens and R. Kaptein Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator O1 through alternative conformations of its DNA-binding domain. EMBO J. 21, 2866-2876 (2002).
S.-T. Hsu, E. Breukink, B. de Kruiff, R. Kaptein, A.M.J.J. Bonvin and N. van Nuland Mapping the targeted membrane pore formation mechanism by solution NMR: the nisin Z and lipid II interaction in SDS micelles. Biochemistry 41, 7670-7676 (2002).
S. Singh, G.E. Folkers, A.M.J.J. Bonvin, R. Boelens, R. Wechselberger, A. Niztayev and R. Kaptein Solution structure and DNA binding properties fo the C-terminal domain of UvrC from E-coli. EMBO J., 21, 6257-6266 (2002).
N. D’Amelio, A.M.J.J Bonvin, M. Czisch, P. Barker and R. Kaptein The C terminus of apocytocrome b562 undergoes fast motions and slow exchange among ordered conformations resembling the folded state Biochemistry, 41, 5505-5514 (2002).

2001

A.M.J.J. Bonvin, K. Houben, M. Guenneugues, R. Kaptein and R. Boelens Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond 15N-13C’ scalar couplings (^3hbJ_NC’). J. Biomol. NMR, 21, 221-233 (2001).

2000

M. van Beest, D. Dooijes, M. van Wetering, S. Kjaerulff, A.M.J.J. Bonvin, O. Nielsen and H. Clevers Sequence-specific HMG box factors recognize 10-12 base pair minor groove motifs. J. Biol. Chem. 275, 27266-27273 (2000).
G. Melacini, A.M.J.J. Bonvin, M. Goodman, R. Boelens and R. Kaptein Hydration dynamics of the collagen triple-helix by NMR. J. Mol. Biol. 300, 1041-1049 (2000).
P.J.A. van Tilborg, M. Czisch, F.A.A. Mulder, G.E. Folkers, A.M.J.J. Bonvin, M. Nair, R. Boelens and R. Kaptein Changes in dynamical behaviour of the retinoid X receptor DNA-binding domain upon binding to 14 base pair DNA half site. Biochemistry 39, 8747-8757 (2000).
A.M.J.J. Bonvin, A.E. Mark and W.F. van Gunsteren The GROMOS96 benchmarks for molecular simulation. Comput. Phys. Commun. 128, 550-557 (2000).
A.M.J.J. Bonvin Localisation and dynamics of sodium counterions around DNA in solution from molecular dynamics simulations. Eur. Biophys. J. 29, 57-60 (2000). (Supplementary material)
A.M.J.J. Bonvin and W.F. van Gunsteren b-hairpin stability and folding: Molecular dynamics studies of the first b-hairpin of tendamistat. J. Mol. Biol. 296 255-268 (2000).
C.J. Oomen, A.M.J.J. Bonvin, S.R. Haseley, P. Hoogerhout, L. van Alphen, J. Kroon and P. Gros Rational design of a subtype-specific peptide vaccine against Neisseria meningitis” In: Proceedings of the 16th American Peptide Symposium: Peptides for a new millenium. ESCOM, Leiden, the Netherlands, 2000, pp. 702-703.

1999

C.A.E.M. Spronk, A.M.J.J. Bonvin, P.K. Radha, G. Melacini, R. Boelens and R. Kaptein The solution structure of lac repressor headpiece 62 complexed to a symmetrical lac operator sequence determined by NMR and restrained molecular dynamics. Structure 7 6472-6480 (1999).
W.F. van Gunsteren, A.M.J.J. Bonvin, X. Daura, L.J. Smith Aspects of modelling biomolecular structure on the basis of spectroscopic or diffraction data. In: Modern techniques in protein NMR, Krishna and Berliner eds., Plenum Publ. Corp. (1999), New York

1998

A.M.J.J. Bonvin, M. Sunnerhagen, G. Otting and W.F. van Gunsteren Water molecules in DNA recognition II: A molecular dynamics view of the structure and hydration of the trp operator. J. Mol. Biol. 282, 859-873 (1998).
M. Sunnerhagen, V.P. Denisov, K. Venu, A.M.J.J. Bonvin, J. Carey, B. Halle and G. Otting Water molecules in DNA recognition I: Hydration lifetimes of the trp operator in solution measured by NMR spectroscopy. J. Mol. Biol. 282, 847-858 (1998).

1997

R. Kaptein, A.M.J.J. Bonvin and R. Boelens Biomolecular structure and dynamics: recent experimental and theoretical advances. In: Proceedings of the Nato Summer School. Eds G. Vergoten and T. Theophanides Kluwer Academic Publisher, 189-209 (1997).

1996

A.M.J.J. Bonvin, R. Boelens and R. Kaptein Protein Structures: Relaxation matrix refinement. In: Encyclopedia of Nuclear Magnetic Resonance Vol. 6. Eds D.M. Grant and R.K. Harris, John Wiley & Sons, 3801-3811 (1996).
M. Slijper, A.M.J.J. Bonvin, R. Boelens and R. Kaptein 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. J. Mol. Biol. 259, 761-773 (1996).
A.M.J.J. Bonvin and A.T. Brunger Do NOE distances contain enough information to assess the relative populations of multi-conformer structures? J. Biomol. NMR. 7, 72-76 (1996).

1995

M. Slijper, A.M.J.J. Bonvin, R. Boelens and R. Kaptein Application of structure refinement using 3D NOE-NOE spectroscopy to lac repressor headpiece (1-56). J. Magn. Reson. B 107, 298-301 (1995).
A.M.J.J. Bonvin and A.T. Brunger Conformational variability of solution nuclear magnetic resonance structures. J. Mol. Biol. 250, 80-93 (1995).
M.A.A. van Tilborg, A.M.J.J. Bonvin, K. Hard, A.L. Davis, B. Maler, R. Boelens and R. Kaptein Structure refinement of the glucocorticoid receptor DNA-binding domain from NMR data by relaxation matrix calculations. J. Mol. Biol. 247, 689-700 (1995).

1994

A.M.J.J. Bonvin, R. Boelens and R. Kaptein Time- and ensemble-averaged direct NOE restraints. J. Biomol. NMR 4, 143-149 (1994).
A.M.J.J. Bonvin, H. Vis, J.N. Breg, M.J.M. Burgering, R. Boelens and R. Kaptein NMR solution structure of the Arc repressor using relaxation matrix calculations. J. Mol. Biol. 236, 328-341 (1994).
A.M.J.J. Bonvin, R. Boelens and R. Kaptein Direct nuclear Overhauser effect refinement of crambin from 2D NMR data using a slow-cooling simulated annealing. Biopolymers 34, 39-50 (1994).

1993

A.M.J.J. Bonvin Determination of biomolecular structures by NMR. Use of relaxation matrix calculations. PhD Thesis, Utrecht University (1993) ISBN 90-393-0408-4.
R.M.A. Knegtel, M. Katahira, J.G. Schilthuis, A.M.J.J. Bonvin, R. Boelens, D. Eib, CHECKCCIP.T. der Saag and R. Kaptein NMR studies of the human retinoic acid receptor-b DNA-binding domain: metal coordination and three dimensional structure. In: “Zinc-finger proteins in oncogenesis. DNA-binding and gene regulation”. M. Sluyser, G. AB, A.O. Brinkmann and R.A. Blankenstein (eds), Annals of the New York Academy of Sciences 684, New York, 49-62 (1993).
A.M.J.J. Bonvin, R. Boelens and R. Kaptein Determination of biomolecular structures by NMR. Use of relaxation matrix calculations. In:”computer simulations of biomolecular systems: theoretical and experimental applications”. Vol.2. W.F. van Gunsteren, P.K. Weiner and A.J. Wilkinson (eds), ESCOM Science Publishers, 407-440 (1993).
A.M.J.J. Bonvin, J.A.C. Rullmann, R.M.J.N. Lamerichs, R. Boelens and R. Kaptein Ensemble Iterative Relaxation Matrix Approach: a new NMR refinement protocol applied to the solution structure of crambin. PROTEINS: Structure, Function & Genetics 15, 385-400 (1993).
R.M.A. Knegtel, M. Katahira, J.G. Schilthuis, A.M.J.J. Bonvin, R. Boelens, D. Eib, P.T. der Saag and R. Kaptein The solution structure of the human retinoic acid receptor-b DNA-binding domain. J. Biomol. NMR 3, 1-17 (1993).

1992

J.A.C. Rullmann, A.M.J.J. Bonvin, R. Boelens and R. Kaptein Structure determination from NMR - Application to crambin In: Computation of biomolecular structures: achievements, problems and perspectives.” (Proceeding of a workshop held at Schloss Ringberg, March 1990), T.M. Jovin and D.M. Soumpasis (eds.), Springer, 1-14 (1992).

1991

A.M.J.J. Bonvin, R. Boelens and R. Kaptein Direct structure refinement using 3D NOE-NOE spectra of biomolecules. J. Magn. Reson. 95, 626-631 (1991).
A.M.J.J. Bonvin, R. Boelens and R. Kaptein Direct NOE refinement of biomolecular structures using 2D NMR data. J. Biomol. NMR 1, 305-309 (1991).
C. Gonzales, J.A.C. Rullmann, A.M.J.J. Bonvin, R. Boelens and R. Kaptein Toward an NMR R factor. J. Magn. Reson. 91, 659-664 (1991).

1990

I. Burghardt , L. Di Bari, A. Bonvin and G. Bodenhausen Effect of strong coupling in multiple-quantum-filtered two-dimensional NOE spectroscopy. J. Magn. Reson. 86, 652-656 (1990).