Karaca Lab. on Computational Structural Biology


Life is operated at the nanometer scale through orchestrated communications of biomolecules. By dissecting this nanoworld, we can acquire a fundamental understanding of how biological macromolecules function, how they are related to disease-linked pathways and how to design drugs targeting them. This understanding led to the birth and rise of Structural Biology, the study of the structures of biomolecules and their complexes at atomic resolution.

Experimental structure determination techniques, X-ray crystallography and Nuclear Magnetic Resonance (NMR) spectroscopy, have solved tens of thousands of structures of biomolecules and their complexes. Still, the field cannot keep pace with the speed at which data are generated in other disciplines, such as genetics, biochemistry and various associated “omics” technologies. Computational structural biology emerged to help overcome this bottleneck and has evolved to generate high-accuracy models of biological macromolecules rapidly.


As a computational structural biology group, we are interested in unveiling the physical principles of biomolecular interactions through determining and/or dissecting the structures of biomolecular complexes. In order to do so, we develop and apply various computational tools, such as docking, homology modelling and molecular dynamics. We also integrate experimental and evolutionary information into our calculations, which we obtain through our collaborations.

Lately, we have been concentrated on understanding:

  • Molecular basis of biomolecular recognition in gene regulation,
  • Impact of single point mutations in the formation of rare diseases,
  • Exploring the structural principles of epigenetic modifications.

We also have been working on predicting new designer sequences to combat COVID-19.

For more please also check our Github Page, Dr. Karaca's Twitter acount or Google Scholar Profile.


Selected presentations:


We are always interested in meeting motivated candidates. Please contact Dr. Karaca to receive up-to-date information on the currently open positions (ezgi.karaca@ibg.edu.tr).


We are affiliated with Dokuz Eylul University's Biomedicine and Health Sciences Graduate Program. For more information on the program, you can contact Dr. Karaca.

Group Members

Karaca Lab. on Computational Structural Biology

Research Group Leader

+90 232 299 41 00 (5041)

Burcu ÖZDEN Research Assistant  burcu.ozden@ibg.edu.tr

Eda ŞAMİLOĞLU Research Assistant  eda.samiloglu@msfr.ibg.edu.tr

Mehdi KOŞACA Research Assistant  mehdi.kosaca@msfr.ibg.edu.tr

Büşra SAVAŞ PhD Student  busra.savas@msfr.ibg.edu.tr

Ayşe Berçin BARLAS PhD Student  aysebercin.barlas@msfr.ibg.edu.tr

Former Members

Mehmet ERGÜVEN Research Assistant  mehmet.erguven@msfr.ibg.edu.tr

Deniz DOĞAN MSc Student  deniz.dogan@msfr.ibg.edu.tr

Tülay KARAKULAK Researcher  tulay.karakulak@ibg.edu.tr

Can YÜKRÜK Visiting Student  can.yukruk@msfr.ibg.edu.tr

Can YÜKRÜK Undergraduate Student  can.yukruk@msfr.ibg.edu.tr

Selected Publications

Azbazdar Y, Ozalp O, Sezgin E, Veerapathiran S, Duncan AL, Sansom MSP, Eggeling C, Wohland T, Karaca E, Ozhan G. More Favorable Palmitic Acid Over Palmitoleic Acid Modification of Wnt3 Ensures Its Localization and Activity in Plasma Membrane Domains. Frontiers in cell and developmental biology. 2019 November ; 7 : 281. doi:10.3389/fcell.2019.00281. Download

Pavlopoulou A, Karaca E, Balestrazzi A, Georgakilas AG. In Silico Phylogenetic and Structural Analyses of Plant Endogenous Danger Signaling Molecules upon Stress. Oxidative medicine and cellular longevity. 2019 July ; 2019 : 8683054. doi:10.1155/2019/8683054. Download

Dafsari HS, Sprute R, Wunderlich G, Daimagüler HS, Karaca E, Contreras A, Becker K, Schulze-Rhonhof M, Kiening K, Karakulak T, Kloss M, Horn A, Pauls A, Nürnberg P, Altmüller J, Thiele H, Assmann B, Koy A, Cirak S. Novel mutations in KMT2B offer pathophysiological insights into childhood-onset progressive dystonia.. Journal of human genetics. 2019 August ; 64 (8) : 803-813. doi:10.1038/s10038-019-0625-1. Download

Bonvin AMJJ, Karaca E, Kastritis PL, Rodrigues JPGLM. Defining distance restraints in HADDOCK. Nature Protocols. 2018 June ; 13 : 1503. doi:10.1038/s41596-018-0017-6. Download

Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork P, Barabas O. Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance. Cell. 2018 March ; 173 (1) : 208-220.e220. doi:10.1016/j.cell.2018.02.032. Download

Ercan I, Tufekci KU, Karaca E, Genc S, Genc K. Peptide Derivatives of Erythropoietin in the Treatment of Neuroinflammation and Neurodegeneration. Advances in Protein Chemistry and Structural Biology. 2018 February ; 112 : 309-357. doi:10.1016/bs.apcsb.2018.01.007. Download

Karaca E, Rodrigues JPGLM, Graziadei A, Bonvin AMJJ, Carlomagno T. M3: an integrative framework for structure determination of molecular machines. Nature methods. 2017 August ; 14 (9) : 897-902. doi:10.1038/nmeth.4392. Download

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 round 1.. Proteins. 2017 March ; 85 (3) : 417-423. doi:10.1002/prot.25198. Download

Bebel A, Karaca E, Kumar B, Stark WM, Barabas O. Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending.. eLife. 2016 December ; 5 . doi:10.7554/eLife.19706. Download

van Zundert GCP, Rodrigues JPGLM, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond ASJ, van Dijk M, de Vries SJ, Bonvin AMJJ. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.. Journal of molecular biology. 2016 February ; 428 (4) : 720-725. doi:10.1016/j.jmb.2015.09.014. Download

Rodrigues JP, Karaca E, Bonvin AM. Information-driven structural modelling of protein-protein interactions.. Methods in molecular biology (Clifton, N.J.). 2015 January ; 1215 : 399-424. doi:10.1007/978-1-4939-1465-4_18. Download

Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, Fernández-Recio J, Xu J, Muthu P, Praneeth Kilambi K, Gray JJ, Grudinin S, Derevyanko G, Mitchell JC, Wieting J, Kanamori E, Tsuchiya Y, Murakami Y, Sarmiento J, Standley DM, Shirota M, Kinoshita K, Nakamura H, Chavent M, Ritchie DW, Park H, Ko J, Lee H, Seok C, Shen Y, Kozakov D, Vajda S, Kundrotas PJ, Vakser IA, Pierce BG, Hwang H, Vreven T, Weng Z, Buch I, Farkash E, Wolfson HJ, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Wojdyla JA, Kleanthous C, Wodak SJ. Blind prediction of interfacial water positions in CAPRI.. Proteins. 2014 April ; 82 (4) : 620-32. doi:10.1002/prot.24439. Download

Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, Eisenstein M, Karczynska A, Czaplewski C, Lubecka E, Lipska A, Krupa P, Mozolewska M, Golon Ł, Samsonov S, Liwo A, Crivelli S, Pagès G, Karasikov M, Kadukova M, Yan Y, Huang SY, Rosell M, Rodríguez-Lumbreras LA, Romero-Durana M, Díaz-Bueno L, Fernandez-Recio J, Christoffer C, Terashi G, Shin WH, Aderinwale T, Maddhuri Venkata Subraman SR, Kihara D, Kozakov D, Vajda S, Porter K, Padhorny D, Desta I, Beglov D, Ignatov M, Kotelnikov S, Moal IH, Ritchie DW, Chauvot de Beauchêne I, Maigret B, Devignes MD, Ruiz Echartea ME, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Cao Y, Shen Y, Baek M, Park T, Woo H, Seok C, Braitbard M, Bitton L, Scheidman-Duhovny D, Dapkūnas J, Olechnovič K, Venclovas Č, Kundrotas PJ, Belkin S, Chakravarty D, Badal VD, Vakser IA, Vreven T, Vangaveti S, Borrman T, Weng Z, Guest JD, Gowthaman R, Pierce BG, Xu X, Duan R, Qiu L, Hou J, Ryan Merideth B, Ma Z, Cheng J, Zou X, Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue L, Jiménez-García B, van Noort CW, Honorato RV, Bonvin AMJJ, Wodak SJ. Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.. Proteins. 2014 December ; 87 (12) : 1200-1221. doi:10.1002/prot.25838. Download

Rodrigues JP, Melquiond AS, Karaca E, Trellet M, van Dijk M, van Zundert GC, Schmitz C, de Vries SJ, Bordogna A, Bonati L, Kastritis PL, Bonvin AM. Defining the limits of homology modeling in information-driven protein docking.. Proteins. 2013 December ; 81 (12) : 2119-28. doi:10.1002/prot.24382. Download

Karaca E, Bonvin AM. On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys.. Acta crystallographica. Section D, Biological crystallography. 2013 May ; 69 (Pt 5) : 683-94. doi:10.1107/S0907444913007063. Download

Karaca E, Bonvin AM. Advances in integrative modeling of biomolecular complexes.. Methods. 2013 March ; 59 (3) : 372-81. doi:10.1016/j.ymeth.2012.12.004. Download

Rodrigues JP, Trellet M, Schmitz C, Kastritis P, Karaca E, Melquiond AS, Bonvin AM. Clustering biomolecular complexes by residue contacts similarity.. Proteins. 2012 July ; 80 (7) : 1810-7. doi:10.1002/prot.24078. Download

Karaca E, Bonvin AM. A multidomain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes.. Structure. 2011 April ; 19 (4) : 555-65. doi:10.1016/j.str.2011.01.014. Download

Karaca E, Tozluoğlu M, Nussinov R, Haliloğlu T. Alternative allosteric mechanisms can regulate the substrate and E2 in SUMO conjugation.. Journal of molecular biology. 2011 March ; 406 (4) : 620-30. doi:10.1016/j.jmb.2010.12.044. Download

Adrien S.J. Melquiond, Ezgi Karaca, Panagiotis L. Kastritis, Alexandre M.J.J. Bonvin. Next challenges in protein–protein docking: from proteome to interactome and beyond. WIREs Computational Molecular Science. 2011 January . doi:10.1002/wcms.91. Download

de Vries SJ, Melquiond AS, Kastritis PL, Karaca E, Bordogna A, van Dijk M, Rodrigues JP, Bonvin AM. Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions.. Proteins. 2010 November ; 78 (15) : 3242-9. doi:10.1002/prot.22814. Download

Karaca E, Melquiond AS, de Vries SJ, Kastritis PL, Bonvin AM. Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server.. Molecular and Cellular proteomics. 2010 August ; 9 (8) : 1784-94. doi:10.1074/mcp.M000051-MCP201. Download

Nicastro G, Todi SV, Karaca E, Bonvin AM, Paulson HL, Pastore A. Understanding the role of the Josephin domain in the PolyUb binding and cleavage properties of ataxin-3.. PloS one. 2010 August ; 5 (8) : e12430. doi:10.1371/journal.pone.0012430. Download

Tozluoğlu M, Karaca E, Nussinov R, Haliloğlu T. A mechanistic view of the role of E3 in sumoylation.. PLoS computational biology. 2010 August ; 6 (8) . doi:10.1371/journal.pcbi.1000913. Download

Tozluoğlu M, Karaca E, Haliloglu T, Nussinov R. Cataloging and organizing p73 interactions in cell cycle arrest and apoptosis.. Nucleic acids research. 2008 September ; 36 (15) : 5033-49. doi:10.1093/nar/gkn481. Download

Total : 25


The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Kornea Endoteli Dokusunun Kök Hücre ve Biyomühendislik Yaklasımlarıyla Geliştirilmesi, Ongoing

The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Interaction of Spesific Insulin Receptor Isoforms with c-Met: Mechanisms and Contributing Roles in the Progression of Hepatocellular Carcinoma, Ongoing

Health Institutes of Turkey- TUSEB - RD : PROT-ON: Structure-based Detection of Critical Mutations in Redesigning Protein-protein Interfaces, Ongoing

The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Epigenetics of Epithelial-to-Mesenchymal and Mesenchymal-to-Epithelial Transitions : Role of Histone Variants and Pioneer Transcription Factors, Ongoing

The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Systematic Approach to Characterize Pioneer Transcription Factor Binding to Chromatin, Finished

European Molecular Biology Organization - EMBO - RD : Identification of Pioneer Transcription Factor Binding Modes to Chromatin, Ongoing

The Scientific and Technological Research Council of Turkey - TUBITAK - RD : İnsan DNA Metiltransferaz 3A Enziminin Çalışma İlkelerinin Hesaplamalı Yöntemlerle Tanımlanması, Finished

The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Development of Recombinant Protein Based Vaccine Against SARS-CoV-2, Ongoing

The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Development of Drugs Based on “Ghost Receptor-Antibody” Against SARS-CoV-2, Ongoing

The Scientific and Technological Research Council of Turkey - TUBITAK - RD : TROPIC: An integrative approach to define druggable human-parasite interactions, Funded, Not Started

Open Positions

We are looking for a post-doc researcher, who is expected to work on molecular modeling and/or method development. If you would like to be considered for the position, here are the main requirements.

  • Extensive experience in molecular modeling OR in a scientific programming language (e.g. Python, MATLAB, R)
  • Ability to work in an interdisciplinary environment.

Please contact ezgi.karaca@ibg.edu.tr and check Karaca Lab main page for further details.

We are looking for a full-time or part-time software engineer, who will be supporting the team in tool development, scripting and web-service design. If you would like to be considered for the position, here are the main requirements:

  • Graduated from Computer Engineering, Software Engineering or Bioinformatics departments OR having an extensive experience in programming.
  • Ability to work in an interdisciplinary environment.

Please contact ezgi.karaca@ibg.edu.tr and check Karaca Lab main page for further details.


  • Installation Grant by EMBO, 2020
  • Young Scientist (BAGEP) Award by Science Academy, 2020
  • Young Investigator Travel Award by eLife Journal, 2019

Academic Memberships

  • Tıp Bilişim Derneği, 2018


Karaca Lab. on Computational Structural Biology

Research Group Leader

+90 232 299 41 00 (5041)