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

Anna Vangone
  • 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 Bioinformatics, Department of Chemistry and Biology, University of Salerno, Italy, 2013

Current position

Marie Skłodowska-Curie Individual fellow (postdoc), Computational Structural Biology group, Utrecht University (NL)

Publications

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. Calvanese, L., D'Auria, G., Vangone, A., Falcigno, L. and Oliva, R. (2016). Analysis of the interface variability in NMR structure ensembles of protein-protein complexes. J Struct Biol 194(3): 317-324.
  7. 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.
  8. Vangone, A. and Bonvin, A. M. (2015). Contacts-based prediction of binding affinity in protein-protein complexes. Elife 4: e07454.
  9. Chermak, E., Petta, A., Serra, L., Vangone, A., Scarano, V., Cavallo, L. and Oliva, R. (2015). CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts. Bioinformatics 31(9): 1481-1483.
  10. Vangone, A., Abdel-Azeim, S., Caputo, I., Sblattero, D., Di Niro, R., Cavallo, L. and Oliva, R. (2014). Structural basis for the recognition in an idiotype-anti-idiotype antibody complex related to celiac disease. PLoS One 9(7): e102839.
  11. Abdel-Azeim, S., Chermak, E., Vangone, A., Oliva, R. and Cavallo, L. (2014). MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories. BMC Bioinformatics 15 Suppl 5: S1.
  12. Kelm, S., Vangone, A., Choi, Y., Ebejer, J. P., Shi, J. and Deane, C. M. (2014). Fragment-based modeling of membrane protein loops: successes, failures, and prospects for the future. Proteins 82(2): 175-186.
  13. Menegatti, M., Vangone, A., Palla, R., Milano, G., Cavallo, L., Oliva, R., De Cristofaro, R. and Peyvandi, F. (2014). A recurrent Gly43Asp substitution in coagulation Factor X rigidifies its catalytic pocket and impairs catalytic activity and intracellular trafficking. Thromb Res 133(3): 481-487.
  14. Vangone, A., Cavallo, L. and Oliva, R. (2013). Using a consensus approach based on the conservation of inter-residue contacts to rank CAPRI models. Proteins 81(12): 2210-2220.
  15. Oliva, R., Vangone, A. and Cavallo, L. (2013). Ranking multiple docking solutions based on the conservation of inter-residue contacts. Proteins 81(9): 1571-1584.
  16. Vangone, A., Oliva, R. and Cavallo, L. (2012). CONS-COCOMAPS: a novel tool to measure and visualize the conservation of inter-residue contacts in multiple docking solutions. BMC Bioinformatics 13 Suppl 4: S19.
  17. Vangone, A., Spinelli, R., Scarano, V., Cavallo, L. and Oliva, R. (2011). COCOMAPS: a web application to analyze and visualize contacts at the interface of biomolecular complexes. Bioinformatics 27(20): 2915-2916.
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: 1649, 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 ...