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Anna Vangone - Publications

Affiliations: 
2013-2017 Utrecht University, Utrecht, Netherlands 
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25 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Schwarz D, Georges G, Kelm S, Shi J, Vangone A, Deane CM. Co-evolutionary Distance Predictions Contain Flexibility Information. Bioinformatics (Oxford, England). PMID 34383892 DOI: 10.1093/bioinformatics/btab562  0.413
2020 Elez K, Bonvin AMJJ, Vangone A. Biological vs. Crystallographic Protein Interfaces: An Overview of Computational Approaches for Their Classification Crystals. 10: 114. DOI: 10.3390/cryst10020114  0.323
2019 Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue LC, Honorato RV, Moreira I, Kurkcuoglu Z, Vangone A, Bonvin AMJJ. An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45. Proteins. PMID 31886559 DOI: 10.1002/Prot.25869  0.655
2019 Jiménez-García B, Elez K, Koukos PI, Bonvin AMJJ, Vangone A. PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes. Bioinformatics (Oxford, England). PMID 31141126 DOI: 10.1093/bioinformatics/btz437  0.726
2019 Vangone A, Schaarschmidt J, Koukos P, Geng C, Citro N, Trellet ME, Xue LC, Bonvin AMJJ. Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server. Bioinformatics (Oxford, England). 35: 1585-1587. PMID 31051038 DOI: 10.1093/bioinformatics/bty816  0.758
2018 Geng C, Vangone A, Folkers GE, Xue LC, Bonvin AMJJ. iSEE: Interface Structure, Evolution and Energy-based machine learning predictor of binding affinity changes upon mutations. Proteins. PMID 30417935 DOI: 10.1002/prot.25630  0.801
2017 Vangone A, Bonvin AMJJ. PRODIGY: A Contact-based Predictor of Binding Affinity in Protein-protein Complexes. Bio-Protocol. 7: e2124. PMID 34458447 DOI: 10.21769/BioProtoc.2124  0.443
2017 Kurkcuoglu Z, Koukos PI, Citro N, Trellet ME, Rodrigues JPGLM, Moreira IS, Roel-Touris J, Melquiond ASJ, Geng C, Schaarschmidt J, Xue LC, Vangone A, Bonvin AMJJ. Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. Journal of Computer-Aided Molecular Design. PMID 28831657 DOI: 10.1007/S10822-017-0049-Y  0.71
2017 Vangone A, Rodrigues JPGLM, Xue LC, van Zundert GCP, Geng C, Kurkcuoglu Z, Nellen M, Narasimhan S, Karaca E, van Dijk M, Melquiond ASJ, Visscher KM, Trellet M, Kastritis PL, Bonvin AMJJ. Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI (page 418). Proteins. 85: 1589-1590. PMID 28730688 DOI: 10.1002/Prot.25339  0.757
2016 de Bruin RC, Stam AG, Vangone A, van Bergen En Henegouwen PM, Verheul HM, Sebestyén Z, Kuball J, Bonvin AM, de Gruijl TD, van der Vliet HJ. Prevention of Vγ9Vδ2 T Cell Activation by a Vγ9Vδ2 TCR Nanobody. Journal of Immunology (Baltimore, Md. : 1950). PMID 27895170 DOI: 10.4049/jimmunol.1600948  0.457
2016 Vangone A, Rodrigues JP, Xue LC, van Zundert GC, Geng C, Kurkcuoglu Z, Nellen M, Narasimhan S, Karaca E, van Dijk M, Melquiond AS, Visscher KM, Trellet M, Kastritis PL, Bonvin AM. Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI Round1. Proteins. PMID 27802573 DOI: 10.1002/Prot.25198  0.742
2016 Xue LC, Rodrigues JP, Kastritis PL, Bonvin AM, Vangone A. PRODIGY: a web server for predicting the binding affinity of protein-protein complexes. Bioinformatics (Oxford, England). PMID 27503228 DOI: 10.1093/Bioinformatics/Btw514  0.813
2016 Geng C, Vangone A, Bonvin AM. Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes. Protein Engineering, Design & Selection : Peds. PMID 27284087 DOI: 10.1093/protein/gzw020  0.807
2016 Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, ... ... Vangone A, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. PMID 27122118 DOI: 10.1002/Prot.25007  0.789
2016 Calvanese L, D'Auria G, Vangone A, Falcigno L, Oliva R. Analysis of the interface variability in NMR structure ensembles of protein-protein complexes. Journal of Structural Biology. 194: 317-24. PMID 26968364 DOI: 10.1016/j.jsb.2016.03.008  0.352
2016 Calvanese L, D'Auria G, Vangone A, Falcigno L, Oliva R. Analysis of the interface variability in NMR structure ensembles of protein-protein complexes. Journal of Structural Biology. 194: 317-24. PMID 26968364 DOI: 10.1016/j.jsb.2016.03.008  0.352
2015 Vreven T, Moal IH, Vangone A, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jiménez-García B, Bates PA, Fernandez-Recio J, Bonvin AM, Weng Z. Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. Journal of Molecular Biology. 427: 3031-41. PMID 26231283 DOI: 10.1016/J.Jmb.2015.07.016  0.789
2015 Vangone A, Bonvin AM. Contacts-based prediction of binding affinity in protein-protein complexes. Elife. 4: e07454. PMID 26193119 DOI: 10.7554/eLife.07454  0.681
2015 Vangone A, Bonvin AM. Contacts-based prediction of binding affinity in protein-protein complexes. Elife. 4: e07454. PMID 26193119 DOI: 10.7554/eLife.07454  0.681
2015 Vangone A, Bonvin AM. Author response: Contacts-based prediction of binding affinity in protein–protein complexes Elife. DOI: 10.7554/Elife.07454.018  0.638
2014 Kelm S, Vangone A, Choi Y, Ebejer JP, Shi J, Deane CM. Fragment-based modeling of membrane protein loops: successes, failures, and prospects for the future. Proteins. 82: 175-86. PMID 23589399 DOI: 10.1002/prot.24299  0.378
2014 Kelm S, Vangone A, Choi Y, Ebejer JP, Shi J, Deane CM. Fragment-based modeling of membrane protein loops: successes, failures, and prospects for the future. Proteins. 82: 175-86. PMID 23589399 DOI: 10.1002/prot.24299  0.378
2013 Vangone A, Cavallo L, Oliva R. Using a consensus approach based on the conservation of inter-residue contacts to rank CAPRI models Proteins: Structure, Function and Bioinformatics. 81: 2210-2220. PMID 24115176 DOI: 10.1002/prot.24423  0.323
2012 Vangone A, Oliva R, Cavallo L. CONS-COCOMAPS: a novel tool to measure and visualize the conservation of inter-residue contacts in multiple docking solutions. Bmc Bioinformatics. 13: S19. PMID 22536965 DOI: 10.1186/1471-2105-13-S4-S19  0.346
2012 Vangone A, Oliva R, Cavallo L. CONS-COCOMAPS: a novel tool to measure and visualize the conservation of inter-residue contacts in multiple docking solutions. Bmc Bioinformatics. 13: S19. PMID 22536965 DOI: 10.1186/1471-2105-13-S4-S19  0.346
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