| The HADDOCK2. 2 web server: user-friendly integrative modeling of biomolecular complexes GCP Van Zundert, J Rodrigues, M Trellet, C Schmitz, PL Kastritis, ... Journal of molecular biology 428 (4), 720-725, 2016 | 2721 | 2016 |
| Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: a CASP‐CAPRI experiment MF Lensink, S Velankar, A Kryshtafovych, SY Huang, ... Proteins: Structure, Function, and Bioinformatics 84, 323-348, 2016 | 168 | 2016 |
| Building macromolecular assemblies by information-driven docking E Karaca, ASJ Melquiond, SJ De Vries, PL Kastritis, AMJJ Bonvin Molecular & Cellular Proteomics 9 (8), 1784-1794, 2010 | 160 | 2010 |
| Clustering biomolecular complexes by residue contacts similarity JP Rodrigues, M Trellet, C Schmitz, P Kastritis, E Karaca, ASJ Melquiond, ... Proteins: Structure, Function, and Bioinformatics 80 (7), 1810-1817, 2012 | 127 | 2012 |
| Advances in integrative modeling of biomolecular complexes E Karaca, AMJJ Bonvin Methods 59 (3), 372-381, 2013 | 85 | 2013 |
| Understanding the role of the Josephin domain in the PolyUb binding and cleavage properties of ataxin-3 G Nicastro, SV Todi, E Karaca, AMJJ Bonvin, HL Paulson, A Pastore PloS one 5 (8), e12430, 2010 | 85 | 2010 |
| Defining the limits of homology modeling in information‐driven protein docking J Rodrigues, ASJ Melquiond, E Karaca, M Trellet, M Van Dijk, ... Proteins: Structure, Function, and Bioinformatics 81 (12), 2119-2128, 2013 | 78 | 2013 |
| A multidomain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes E Karaca, AMJJ Bonvin Structure 19 (4), 555-565, 2011 | 77 | 2011 |
| On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys E Karaca, AMJJ Bonvin Biological Crystallography 69 (5), 683-694, 2013 | 72 | 2013 |
| The HADDOCK2. 4 web server for integrative modeling of biomolecular complexes RV Honorato, ME Trellet, B Jiménez-García, JJ Schaarschmidt, M Giulini, ... Nature protocols 19 (11), 3219-3241, 2024 | 65 | 2024 |
| Blind prediction of interfacial water positions in CAPRI MF Lensink, IH Moal, PA Bates, PL Kastritis, ASJ Melquiond, E Karaca, ... Proteins: Structure, Function, and Bioinformatics 82 (4), 620-632, 2014 | 63 | 2014 |
| Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1 A Vangone, J Rodrigues, LC Xue, GCP Van Zundert, C Geng, ... Proteins: Structure, Function, and Bioinformatics 85 (3), 417-423, 2017 | 62 | 2017 |
| Strengths and weaknesses of data‐driven docking in critical assessment of prediction of interactions SJ de Vries, ASJ Melquiond, PL Kastritis, E Karaca, A Bordogna, ... Proteins: Structure, Function, and Bioinformatics 78 (15), 3242-3249, 2010 | 55 | 2010 |
| Transposase-DNA complex structures reveal mechanisms for conjugative transposition of antibiotic resistance A Rubio-Cosials, EC Schulz, L Lambertsen, G Smyshlyaev, ... Cell 173 (1), 208-220. e20, 2018 | 50 | 2018 |
| Assessment of the CASP14 assembly predictions B Ozden, A Kryshtafovych, E Karaca Proteins: Structure, Function, and Bioinformatics 89 (12), 1787-1799, 2021 | 38 | 2021 |
| M3: an integrative framework for structure determination of molecular machines E Karaca, JP Rodrigues, A Graziadei, AMJJ Bonvin, T Carlomagno Nature methods 14 (9), 897-902, 2017 | 38 | 2017 |
| A mechanistic view of the role of E3 in sumoylation M Tozluoğlu, E Karaca, R Nussinov, T Haliloğlu PLoS computational biology 6 (8), e1000913, 2010 | 37 | 2010 |
| Next challenges in protein–protein docking: from proteome to interactome and beyond ASJ Melquiond, E Karaca, PL Kastritis, AMJJ Bonvin Wiley Interdisciplinary Reviews: Computational Molecular Science 2 (4), 642-651, 2012 | 33 | 2012 |
| The impact of AI‐based modeling on the accuracy of protein assembly prediction: insights from CASP15 B Ozden, A Kryshtafovych, E Karaca Proteins: Structure, Function, and Bioinformatics 91 (12), 1636-1657, 2023 | 30 | 2023 |
| Cataloging and organizing p73 interactions in cell cycle arrest and apoptosis M Tozluoğlu, E Karaca, T Haliloglu, R Nussinov Nucleic acids research 36 (15), 5033-5049, 2008 | 29 | 2008 |
Alexandre M.J.J. BonvinUtrecht universityPatvirtintas el. paštas uu.nl
