Karaca Lab. on Computational Structural Biology

Experimental structure determination techniques 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 to generate high-accuracy structural models rapidly. 

Since late 2020, we have been witnessing a revolution in structure prediction with the emergence of AlphaFold. Together with AF and other related AI-based tools, we are closer more than ever to interpreting the omics data at the structural level. In our lab, we are developing tools and approaches to assist this interpretation by bridging information accumulating at different scales.

RESEARCH INTERESTS

Lately, we have been concentrating on:

  • Finding the optimal mutations for designing new protein binders. For more please check our PROT-ON's web server.
  • Understanding partner-selecting interactions among paralog protein-protein complexes, such as in the TAM-ligand system.
  • Introducing dynamics info into integrative approaches to study large and intricate systems, like PTF:nucleosome complexes.
  • Explaining the impact of isoforms/mutations on protein interactions, as in eukaryotic translation.
  • Last but not least, how CASP predictors have been performing on multimeric predictions. Dr. Karaca has been acting as the CASP assembly assessor since the 14th round of CASP. For more, please see the CASP website and our evaluation paper on the 14th round of CASP.

You can also check our Github Page, Dr. Karaca's Twitter acount or her Google Scholar Profile.

BRIEF CV of the PI

Education:

  • Ph.D. in Computational Structural Biology, Utrecht University (Bonvin Lab, the Netherlands)
  • M.Sc. & B.Sc. in Chemical Engineering, Bogazici University (Haliloglu Lab, Türkiye)

Experience:

  • Since 2017 Asst. Prof. in Dokuz Eylul University & PI in Izmir Biomedicine and Genome Center
  • 2013-2016 EMBL Heidelberg (Carlomagno & Barabas Labs, Germany)
  • 2006-2007, Summer terms, NCI (USA, Nussinov Lab)

OUTREACH ACTIVITIES

Selected presentations:

Group Members

Karaca Lab. on Computational Structural Biology

Research Group Leader

Ezgi KARACA
ezgi.karaca@ibg.edu.tr
+90 232 299 41 00 (5041)

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


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


İrem YILMAZBİLEK MSc Student  irem.yilmazbilek@ibg.edu.tr


Mehdi KOŞACA PhD Student  mehdi.kosaca@ibg.edu.tr


Beyza KAYNARCA Undergraduate Student  beyza.kaynarca@ibg.edu.tr


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


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


Former Members

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


Melis OKTAYOĞLU Undergraduate Student  melis.oktayoglu@ibg.edu.tr


İrem YILMAZBİLEK Undergraduate Student  irem.yilmazbilek@ibg.edu.tr


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


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


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


Aleyna Dilan KIRAN Undergraduate Student  aleyna.kiran@msfr.ibg.edu.tr


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


Aybike ERDOĞAN PhD Student  aybike.erdogan@ibg.edu.tr


Atakan ÖZSAN Undergraduate Student  atakan.ozsan@ibg.edu.tr


Selected Publications

Erguven M, Kilic S, Karaca E, Diril MK.. Genetic complementation screening and molecular docking give new insight on phosphorylation-dependent Mastl kinase activation. Journal of Biomolecular Structure and Dynamics. 2022 October . doi:10.1080/07391102.2022.2131627. Download

Karaca E, Prévost C, Sacquin-Mora S. Modeling the Dynamics of Protein-Protein Interfaces, How and Why?. Molecules (Basel, Switzerland). 2022 March ; 27 (6) : 1841. doi:10.3390/molecules27061841. Download

Erguven M, Karakulak T, Diril MK, Karaca E. How Far Are We from the Rapid Prediction of Drug Resistance Arising Due to Kinase Mutations?. ACS omega. 2021 January ; 6 (2) : 1254-1265. doi:10.1021/acsomega.0c04672. Download

Karakulak T, Rifaioglu AS, Rodrigues JPGLM, Karaca E. Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl. Frontiers in Molecular Biosciences. 2021 June (8:658906) . doi:10.3389/fmolb.2021.658906. Download

Serdal Gungor, Yavuz Oktay, Semra Hiz, Álvaro Aranguren-Ibáñez, Ipek Kalafatcilar, Ahmet Yaramis, Ezgi Karaca, Uluc Yis, Ece Sonmezler, Burcu Ekinci, Mahmut Aslan, Elmasnur Yilmaz, Sunitha Balaraju, Nora Szabo, Steven Laurie, Sergi Beltran, Daniel G. MacArthur, Denisa Hathazi, Rita Horvath. Autosomal recessive variants in TUBGCP2 alter the γ-tubulin ring complex leading to neurodevelopmental disease. iScience. 2021 January ; 24 (1) . doi:10.1016/j.isci.2020.101948. Download

Ozden B, Kryshtafovych A, Karaca E. Assessment of the CASP14 assembly predictions.. Proteins. 2021 August . doi:10.1002/prot.26199. Download

Circir A, Koksal Bicakci G, Savas B, Doken DN, Henden ŞO, Can T, Karaca E, Erson-Bensan AE. A C-term truncated EIF2Bγ protein encoded by an intronically polyadenylated isoform introduces unfavorable EIF2Bγ-EIF2γ interactions.. Proteins. 2021 November . doi:10.1002/prot.26284. Download

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

Athanasia Pavlopoulou, Ezgi Karaca, Alma Balestrazzi, Alexandros G. Georgakilas. InSilicoPhylogenetic andStructural Analysis ofPlant Damps. Preprints. 2018 July ; 2018070522 : 1-14. doi:10.20944/preprints201807.0522.v1. 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 : 33

Projects

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, Ongoing

Open Positions

POST-DOCTORAL RESEARCHER
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.

SOFTWARE ENGINEER
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.

Awards

  • 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

Contact

Karaca Lab. on Computational Structural Biology

Research Group Leader

Ezgi KARACA
ezgi.karaca@ibg.edu.tr
+90 232 299 41 00 (5041)