List of publications of Alexandre M.J.J. Bonvin:


  1. 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., in press (2012).

  2. 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., in press (2012).

  3. 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.

  4. 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).

  5. 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)

  6. 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

  7. S.J Fleishman, et al.
    "Community-wide assessment of protein-interface modeling suggests improvements to design methodology.
    J. Mol. Biol., 414, 289-302 (2011).

  8. 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, Advanced Online Publication.

  9. 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)

  10. C. Schmitz and A.M.J.J. Bonvin
    "Protein-Protein HADDocking using exclusively Pseudocontact Shifts."
    J. Biomol. NMR, 50, 263-266 (2011).

  11. 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).

  12. 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).

  13. 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).

  14. 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).

  15. 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).

  16. 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).

  17. 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).

  18. 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.

  19. 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).

  20. 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.

  21. 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).

  22. 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).

  23. 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.

  24. 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.

  25. 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

  26. 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.

  27. 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. Acid Res., 38, 5634-5647 (2010).

  28. 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).

  29. 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).
    Download the final author version here.

  30. 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).

  31. 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).

  32. 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).

  33. 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).

  34. 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).

  35. 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).

  36. 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).

  37. M. van Dijk and A.M.J.J. Bonvin
    "3D-DART: a DNA structure modelling server."
    Nucl. Adic Res., 37, W235-W239 (2009).

  38. 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).

  39. 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).

  40. 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).

  41. 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).

  42. 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).

  43. 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).

  44. 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).

  45. 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.

  46. 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).

  47. 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).

  48. 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).

  49. 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).

  50. 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).

  51. 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).

  52. 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).

  53. 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).

  54. 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).

  55. 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).

  56. 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).

  57. 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).

  58. 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).

  59. 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).

  60. 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).

  61. 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).

  62. 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).

  63. 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).

  64. 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).

  65. A.M.J.J. Bonvin
    "Flexible protein-protein docking."
    Curr. Opin. Struct. Biol., 16, 194-200 (2006).

  66. 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).

  67. 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).

  68. 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).

  69. 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).

  70. 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).

  71. A.M.J.J. Bonvin, R. Boelens and R. Kaptein
    "NMR analysis of protein interactions"
    Curr. Opin. Chem. Biol., 9, 501-508 (2005).

  72. 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).

  73. 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).

  74. 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).

  75. 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).

  76. 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).

  77. 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).

  78. 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).

  79. 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).

  80. 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).

  81. 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).

  82. 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).

  83. 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).

  84. 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).

  85. 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).

  86. 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).

  87. 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).

  88. 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).

  89. 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).

  90. 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).

  91. 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).

  92. 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).

  93. 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).

  94. 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).

  95. 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).

  96. 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).

  97. 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).

  98. 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).

  99. 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).

  100. 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).

  101. 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).

  102. 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).

  103. 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).

  104. 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 (3hbJNC')."
    J. Biomol. NMR, 21, 221-233 (2001).

  105. 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).

  106. 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).

  107. 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).

  108. 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).

  109. 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)

  110. 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).

  111. 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.

  112. 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).

  113. 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

  114. 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).

  115. 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).

  116. 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).

  117. 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).

  118. 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).

  119. 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).

  120. 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).

  121. A.M.J.J. Bonvin and A.T. Brunger
    "Conformational variability of solution nuclear magnetic resonance structures."
    J. Mol. Biol. 250, 80-93 (1995).

  122. 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).

  123. A.M.J.J. Bonvin, R. Boelens and R. Kaptein
    "Time- and ensemble-averaged direct NOE restraints."
    J. Biomol. NMR 4, 143-149 (1994).

  124. 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).

  125. 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).

  126. 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.

  127. 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
    "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).

  128. 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).

  129. 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).

  130. 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).

  131. 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).

  132. 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).

  133. 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).

  134. 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).

  135. 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).


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