Ezgi Karaca
Ezgi Karaca
Assistant Professor, Izmir Biomedicine and Genome Center
Geverifieerd e-mailadres voor ibg.edu.tr - Homepage
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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
7522016
Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server
E Karaca, ASJ Melquiond, SJ De Vries, PL Kastritis, AMJJ Bonvin
Molecular & Cellular Proteomics 9 (8), 1784-1794, 2010
1212010
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
1062016
Advances in integrative modeling of biomolecular complexes
E Karaca, AMJJ Bonvin
Methods 59 (3), 372-381, 2013
702013
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
692012
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
652010
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
612011
On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys
E Karaca, AMJJ Bonvin
Acta Crystallographica Section D: Biological Crystallography 69 (5), 683-694, 2013
582013
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
512013
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
452014
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
452010
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
302012
A mechanistic view of the role of E3 in sumoylation
M Tozluoğlu, E Karaca, R Nussinov, T Haliloğlu
PLoS Comput Biol 6 (8), e1000913, 2010
262010
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
232017
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
232008
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
212018
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
192017
Alternative allosteric mechanisms can regulate the substrate and E2 in SUMO conjugation
E Karaca, M Tozluoğlu, R Nussinov, T Haliloğlu
Journal of molecular biology 406 (4), 620-630, 2011
112011
Defining distance restraints in HADDOCK
AMJJ Bonvin, E Karaca, PL Kastritis, JP Rodrigues
Nature protocols 13 (7), 1503-1503, 2018
92018
Information-driven structural modelling of protein–protein interactions
JP Rodrigues, E Karaca, AMJJ Bonvin
Molecular modeling of proteins, 399-424, 2015
92015
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