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Coauthors
Anna Vangone Computational Structural Biology group, Bijvoet Center for Biomolecular Research, Faculty of Science Chemistry, Utrecht University, the Netherlands
1 protocol

Alexandre M. J. J. Bonvin
  • Computational Structural Biology group, Bijvoet Center for Biomolecular Research, Faculty of Science Chemistry, Utrecht University, the Netherlands
Contributions
  • 1 Author merit

Education

Ph.D in Chemistry "cum laude", Utrecht University, Netherlands, 1993

Current position

Professor of Computational Structural Biology, Faculty of Science/Chemistry, Utrecht University

Publications (since 2015)

  1. Bohnuud, T., Luo, L., Wodak, S. J., Bonvin, A. M., Weng, Z., Vajda, S., Schueler-Furman, O. and Kozakov, D. (2017). A benchmark testing ground for integrating homology modeling and protein docking. Proteins 85(1): 10-16.
  2. de Bruin, R. C., Stam, A. G., Vangone, A., van Bergen En Henegouwen, P. M., Verheul, H. M., Sebestyen, Z., Kuball, J., Bonvin, A. M., de Gruijl, T. D. and van der Vliet, H. J. (2017). Prevention of Vgamma9Vdelta2 T Cell Activation by a Vgamma9Vdelta2 TCR Nanobody. J Immunol 198(1): 308-317.
  3. van Zundert, G. C., Trellet, M., Schaarschmidt, J., Kurkcuoglu, Z., David, M., Verlato, M., Rosato, A. and Bonvin, A. M. (2016). The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes. J Mol Biol.
  4. Vangone, A., Rodrigues, J. P., Xue, L. C., van Zundert, G. C., Geng, C., Kurkcuoglu, Z., Nellen, M., Narasimhan, S., Karaca, E., van Dijk, M., Melquiond, A. S., Visscher, K. M., Trellet, M., Kastritis, P. L. and Bonvin, A. M. (2016). Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1. Proteins.
  5. Grinter, R., Josts, I., Mosbahi, K., Roszak, A. W., Cogdell, R. J., Bonvin, A. M., Milner, J. J., Kelly, S. M., Byron, O., Smith, B. O. and Walker, D. (2016). Structure of the bacterial plant-ferredoxin receptor FusA. Nat Commun 7: 13308.
  6. Felix, J., Kandiah, E., De Munck, S., Bloch, Y., van Zundert, G. C., Pauwels, K., Dansercoer, A., Novanska, K., Read, R. J., Bonvin, A. M., Vergauwen, B., Verstraete, K., Gutsche, I. and Savvides, S. N. (2016). Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF. Nat Commun 7: 13228.
  7. Spiliotopoulos, D., Kastritis, P. L., Melquiond, A. S., Bonvin, A. M., Musco, G., Rocchia, W. and Spitaleri, A. (2016). dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking. Front Mol Biosci 3: 46.
  8. Xue, L. C., Rodrigues, J. P., Kastritis, P. L., Bonvin, A. M. and Vangone, A. (2016). PRODIGY: a web server for predicting the binding affinity of protein-protein complexes. Bioinformatics 32(23): 3676-3678.
  9. Melo, R., Fieldhouse, R., Melo, A., Correia, J. D., Cordeiro, M. N., Gumus, Z. H., Costa, J., Bonvin, A. M. and Moreira, I. S. (2016). A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces. Int J Mol Sci 17(8).
  10. van Zundert, G. C. and Bonvin, A. M. (2016). Defining the limits and reliability of rigid-body fitting in cryo-EM maps using multi-scale image pyramids. J Struct Biol 195(2): 252-258.
  11. Liu, Y., Rodrigues, J. P., Bonvin, A. M., Zaal, E. A., Berkers, C. R., Heger, M., Gawarecka, K., Swiezewska, E., Breukink, E. and Egmond, M. R. (2016). New Insight into the Catalytic Mechanism of Bacterial MraY from Enzyme Kinetics and Docking Studies. J Biol Chem 291(29): 15057-15068.
  12. Geng, C., Vangone, A. and Bonvin, A. M. (2016). Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes. Protein Eng Des Sel 29(8): 291-299.
  13. Xue, L. C., Rodrigues, J. P. G. L. M., Dobbs, D., Honavar, V. and Bonvin, A. M. J. J. (2016). Template-based protein–protein docking exploiting pairwise interfacial residue restraints. Brief Bioinform.
  14. Lensink, M. F., Velankar, S., Kryshtafovych, A., Huang, S. Y., Schneidman-Duhovny, D., Sali, A., Segura, J., Fernandez-Fuentes, N., Viswanath, S., Elber, R., Grudinin, S., Popov, P., Neveu, E., Lee, H., Baek, M., Park, S., Heo, L., Rie Lee, G., Seok, C., Qin, S., Zhou, H. X., Ritchie, D. W., Maigret, B., Devignes, M. D., Ghoorah, A., Torchala, M., Chaleil, R. A., Bates, P. A., Ben-Zeev, E., Eisenstein, M., Negi, S. S., Weng, Z., Vreven, T., Pierce, B. G., Borrman, T. M., Yu, J., Ochsenbein, F., Guerois, R., Vangone, A., Rodrigues, J. P., van Zundert, G., Nellen, M., Xue, L., Karaca, E., Melquiond, A. S., Visscher, K., Kastritis, P. L., Bonvin, A. M., Xu, X., Qiu, L., Yan, C., Li, J., Ma, Z., Cheng, J., Zou, X., Shen, Y., Peterson, L. X., Kim, H. R., Roy, A., Han, X., Esquivel-Rodriguez, J., Kihara, D., Yu, X., Bruce, N. J., Fuller, J. C., Wade, R. C., Anishchenko, I., Kundrotas, P. J., Vakser, I. A., Imai, K., Yamada, K., Oda, T., Nakamura, T., Tomii, K., Pallara, C., Romero-Durana, M., Jimenez-Garcia, B., Moal, I. H., Fernandez-Recio, J., Joung, J. Y., Kim, J. Y., Joo, K., Lee, J., Kozakov, D., Vajda, S., Mottarella, S., Hall, D. R., Beglov, D., Mamonov, A., Xia, B., Bohnuud, T., Del Carpio, C. A., Ichiishi, E., Marze, N., Kuroda, D., Roy Burman, S. S., Gray, J. J., Chermak, E., Cavallo, L., Oliva, R., Tovchigrechko, A. and Wodak, S. J. (2016). Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins 84 Suppl 1: 323-348.
  15. Meyer, P. A., Socias, S., Key, J., Ransey, E., Tjon, E. C., Buschiazzo, A., Lei, M., Botka, C., Withrow, J., Neau, D., Rajashankar, K., Anderson, K. S., Baxter, R. H., Blacklow, S. C., Boggon, T. J., Bonvin, A. M., Borek, D., Brett, T. J., Caflisch, A., Chang, C. I., Chazin, W. J., Corbett, K. D., Cosgrove, M. S., Crosson, S., Dhe-Paganon, S., Di Cera, E., Drennan, C. L., Eck, M. J., Eichman, B. F., Fan, Q. R., Ferre-D'Amare, A. R., Fromme, J. C., Garcia, K. C., Gaudet, R., Gong, P., Harrison, S. C., Heldwein, E. E., Jia, Z., Keenan, R. J., Kruse, A. C., Kvansakul, M., McLellan, J. S., Modis, Y., Nam, Y., Otwinowski, Z., Pai, E. F., Pereira, P. J., Petosa, C., Raman, C. S., Rapoport, T. A., Roll-Mecak, A., Rosen, M. K., Rudenko, G., Schlessinger, J., Schwartz, T. U., Shamoo, Y., Sondermann, H., Tao, Y. J., Tolia, N. H., Tsodikov, O. V., Westover, K. D., Wu, H., Foster, I., Fraser, J. S., Maia, F. R., Gonen, T., Kirchhausen, T., Diederichs, K., Crosas, M. and Sliz, P. (2016). Data publication with the structural biology data grid supports live analysis. Nat Commun 7: 10882.
  16. Jung, S., Fischer, J., Spudy, B., Kerkow, T., Sonnichsen, F. D., Xue, L., Bonvin, A. M., Goettig, P., Magdolen, V., Meyer-Hoffert, U. and Grotzinger, J. (2016). The solution structure of the kallikrein-related peptidases inhibitor SPINK6. Biochem Biophys Res Commun 471(1): 103-108.
  17. Deplazes, E., Davies, J., Bonvin, A. M., King, G. F. and Mark, A. E. (2016). Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion Channel (ASIC) 1a. J Chem Inf Model 56(1): 127-138.
  18. Rodrigues, J. P., Melquiond, A. S. and Bonvin, A. M. (2016). Molecular dynamics characterization of the conformational landscape of small peptides: A series of hands-on collaborative practical sessions for undergraduate students. Biochem Mol Biol Educ 44(2): 160-167.
  19. van Zundert, G. C., Rodrigues, J. P., Trellet, M., Schmitz, C., Kastritis, P. L., Karaca, E., Melquiond, A. S., van Dijk, M., de Vries, S. J. and Bonvin, A. M. (2016). The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. J Mol Biol 428(4): 720-725.
  20. Zhang, R., Eckert, T., Lutteke, T., Hanstein, S., Scheidig, A., Bonvin, A. M., Nifantiev, N. E., Kozar, T., Schauer, R., Enani, M. A. and Siebert, H. C. (2016). Structure-Function Relationships of Antimicrobial Peptides and Proteins with Respect to Contact Molecules on Pathogen Surfaces. Curr Top Med Chem 16(1): 89-98.
  21. Kalia, M., Willkomm, S., Claussen, J. C., Restle, T. and Bonvin, A. M. (2015). Novel Insights into Guide RNA 5'-Nucleoside/Tide Binding by Human Argonaute 2. Int J Mol Sci 17(1).
  22. Xue, L. C., Dobbs, D., Bonvin, A. M. and Honavar, V. (2015). Computational prediction of protein interfaces: A review of data driven methods. FEBS Lett 589(23): 3516-3526.
  23. Marino, F., Bern, M., Mommen, G. P., Leney, A. C., van Gaans-van den Brink, J. A., Bonvin, A. M., Becker, C., van Els, C. A. and Heck, A. J. (2015). Extended O-GlcNAc on HLA Class-I-Bound Peptides. J Am Chem Soc 137(34): 10922-10925.
  24. Vreven, T., Moal, I. H., Vangone, A., Pierce, B. G., Kastritis, P. L., Torchala, M., Chaleil, R., Jimenez-Garcia, B., Bates, P. A., Fernandez-Recio, J., Bonvin, A. M. and Weng, Z. (2015). Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. J Mol Biol 427(19): 3031-3041.
  25. Vangone, A. and Bonvin, A. M. (2015). Contacts-based prediction of binding affinity in protein-protein complexes. Elife 4: e07454.
  26. Rad-Malekshahi, M., Visscher, K. M., Rodrigues, J. P., de Vries, R., Hennink, W. E., Baldus, M., Bonvin, A. M., Mastrobattista, E. and Weingarth, M. (2015). The Supramolecular Organization of a Peptide-Based Nanocarrier at High Molecular Detail. J Am Chem Soc 137(24): 7775-7784.
  27. van Zundert, G. C. and Bonvin, A. M. (2015). DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes. Bioinformatics 31(19): 3222-3224.
  28. Duarte, A. M., Psomopoulos, F. E., Blanchet, C., Bonvin, A. M., Corpas, M., Franc, A., Jimenez, R. C., de Lucas, J. M., Nyronen, T., Sipos, G. and Suhr, S. B. (2015). Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis. Front Genet 6: 197.
  29. Sali, A., Berman, H. M., Schwede, T., Trewhella, J., Kleywegt, G., Burley, S. K., Markley, J., Nakamura, H., Adams, P., Bonvin, A. M., Chiu, W., Peraro, M. D., Di Maio, F., Ferrin, T. E., Grunewald, K., Gutmanas, A., Henderson, R., Hummer, G., Iwasaki, K., Johnson, G., Lawson, C. L., Meiler, J., Marti-Renom, M. A., Montelione, G. T., Nilges, M., Nussinov, R., Patwardhan, A., Rappsilber, J., Read, R. J., Saibil, H., Schroder, G. F., Schwieters, C. D., Seidel, C. A., Svergun, D., Topf, M., Ulrich, E. L., Velankar, S. and Westbrook, J. D. (2015). Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure 23(7): 1156-1167.
  30. van der Schot, G. and Bonvin, A. M. (2015). Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR. J Biomol NMR 62(4): 497-502.
  31. Sinnige, T., Weingarth, M., Daniels, M., Boelens, R., Bonvin, A. M., Houben, K. and Baldus, M. (2015). Conformational Plasticity of the POTRA 5 Domain in the Outer Membrane Protein Assembly Factor BamA. Structure 23(7): 1317-1324.
  32. van Zundert, G. C. P. and Bonvin, A. M. J. J. (2015). Fast and sensitive rigid-body fitting into cryo-EM density maps with PowerFit. AIMS Biophysics 2: 73-87.
  33. Brewer, K. D., Bacaj, T., Cavalli, A., Camilloni, C., Swarbrick, J. D., Liu, J., Zhou, A., Zhou, P., Barlow, N., Xu, J., Seven, A. B., Prinslow, E. A., Voleti, R., Haussinger, D., Bonvin, A. M., Tomchick, D. R., Vendruscolo, M., Graham, B., Sudhof, T. C. and Rizo, J. (2015). Dynamic binding mode of a Synaptotagmin-1-SNARE complex in solution. Nat Struct Mol Biol 22(7): 555-564.
  34. van Zundert, G. C., Melquiond, A. S. and Bonvin, A. M. (2015). Integrative Modeling of Biomolecular Complexes: HADDOCKing with Cryo-Electron Microscopy Data. Structure 23(5): 949-960.
  35. Kaplan, M., Cukkemane, A., van Zundert, G. C., Narasimhan, S., Daniels, M., Mance, D., Waksman, G., Bonvin, A. M., Fronzes, R., Folkers, G. E. and Baldus, M. (2015). Probing a cell-embedded megadalton protein complex by DNP-supported solid-state NMR. Nat Methods 12(7): 649-652.
  36. Visscher, K. M., Kastritis, P. L. and Bonvin, A. M. (2015). Non-interacting surface solvation and dynamics in protein-protein interactions. Proteins 83(3): 445-458.
1 Protocol published
PRODIGY: A Contact-based Predictor of Binding Affinity in Protein-protein Complexes
Authors:  Anna Vangone and Alexandre M. J. J. Bonvin, date: 02/05/2017, view: 1937, Q&A: 0
Biomolecular interactions between proteins regulate and control almost every biological process in the cell. Understanding these interactions is therefore a crucial step in the investigation of biological systems and in drug design. Many efforts ...