EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

E-mail: ezgi.karaca@embl.de

Publications

Total: 16 publication(s)

2015

Rodrigues JPGLM, Karaca E, Bonvin AMJJ. (2015)

Information-Driven Structural Modelling of Protein–Protein Interactions

In: Kukol A, Molecular Modeling of Proteins. Molecular Modeling of Proteins, vol Part IV. Springer Science. pp 399-424. doi:10.1007/978-1-4939-1465-4_18
doi


2013

Karaca E. (2013)

Dissecting Biomolecular Interactions by Integrative Modeling - PhD Thesis


Karaca E, Bonvin AMJJ. (2013)

On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys

Acta Crystallogr. D Biol. Crystallogr. 69(5):683-694. doi:10.1107/S0907444913007063
doi

Rodrigues JPGLM, Melquiond ASJ, Karaca E, Trellet M, van Dijk M, Zundert GCP, Schmitz C, Vries SJ, Bordogna A, Bonati L, Kastritis PL, Bonvin AMJJ. (2013)

Defining the limits of homology modeling in information‐driven protein docking

Proteins doi:10.1002/prot.24382
doi

Karaca E, Bonvin AMJJ. (2013)

Advances in integrative modeling of biomolecular complexes

Methods 59(3) doi:10.1016/j.ymeth.2012.12.004
doi

Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond ASJ, Karaca E at al. (2013)

Blind prediction of interfacial water positions in CAPRI

Proteins 82(4):620-632. doi:10.1002/prot.24439
doi


2012

Rodrigues JP, Trellet M, Schmitz C, Kastritis P, Karaca E, Melquiond AS, Bonvin AM. (2012)

Clustering biomolecular complexes by residue contacts similarity

Proteins 80(7):1810-1817. doi:10.1002/prot.24078
Europe PMC | doi

Melquiond AS, Karaca E, Kastritis PL, Bonvin AM. (2012)

Next challenges in protein-protein docking: from proteome to interactome and beyond

Wiley Interdiscip Rev Comput Mol Sci 2(4) doi:10.1002/wcms.91
doi

Schmitz C, Melquiond AS, Vries SJ, Karaca E, Dijk M, Kastritis PL, Bonvin AM. (2012)

Protein-Protein Docking with HADDOCK

In: Ivano Bertini, Kathleen S. McGreevy, Giacomo Parigi, NMR of Biomolecules: Towards Mechanistic Systems Biology. Wiley-VCH Verlag GmbH & Co. KGaA. pp 520-535. doi:10.1002/9783527644506
doi


2011

Karaca E, Bonvin AMJJ. (2011)

A multidomain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes

Structure 19(5):555-565. doi:10.1016/j.str.2011.01.014
doi

Karaca E, Tozluoglu M, Nussinov R, Haliloglu T. (2011)

Alternative allosteric mechanisms can regulate the substrate and E2 in SUMO conjugation

PLoS Computational Biology 406(4) doi:10.1016/j.jmb.2010.12.044
doi


2010

de Vries SJ, Melquiond AS, Kastritis PL, Karaca E, Bordogna A, van Dijk M, Rodrigues JP, Bonvin AM. (2010)

Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions

Proteins 78(15):3242-3249. doi:10.1002/prot.22814
Europe PMC | doi

Karaca E, Melquiond AS, Vries SJ, Kastritis PL, Bonvin AM. (2010)

Building Macromolecular Assemblies by Information-driven Docking INTRODUCING THE HADDOCK MULTIBODY DOCKING SERVER

Molecular and Cellular Proteomics 9(8) doi:10.1074/mcp.M000051-MCP201
doi

Nicastro G, Todi SV, Karaca E, Bonvin AM, Paulson HL, Pastore A. (2010)

Understanding the role of the Josephin domain in the PolyUb binding and cleavage properties of ataxin-3

PLoS ONE 5(8) doi:10.1371/journal.pone.0012430
doi

Tozluoglu M, Karaca E, Nussinov R, Haliloglu T. (2010)

A Mechanistic View of the Role of E3 in Sumoylation

PLoS Computational Biology 6(8) doi:10.1371/journal.pcbi.1000913
doi


2008

Tozluoglu M, Karaca E, Haliloglu T, Nussinov R. (2008)

Cataloging and organizing p73 interactions in cell cycle arrest and apoptosis

Nucleic Acids Research 36(15) doi:10.1093/nar/gkn481
doi