1. Home
  2. Research
  3. BASIC AND TRANSLATIONAL RESEARCH PROGRAM
  4. Karaca Lab. on Computational Structural Biology


BASIC AND TRANSLATIONAL RESEARCH PROGRAM
Alotaibi Lab. Angelov Lab. Atabey Lab. Gene Targeting and Transgenic Models Platform Genc Lab. Kale Lab. Karaca Lab. Kucuk Lab. Oktay Lab. Ozhan Lab. Pavlopoulou Lab. Sag Lab. Senturk Lab. Wingender Lab. MG Lab. THORLAB Erkek Lab. BG Lab. Özbek Lab.

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 witnessed a revolution in structure prediction with the emergence of AlphaFold. Together with AF and other AI-based tools, we are closer to interpreting the omics data at the structural level than ever. In our lab, we are developing computational tools and approaches to assist this interpretation by focusing on the structure-function relationships of biomolecular complexes.

 

Research Interests

We are particularly interested in understanding the role of dynamics and variations across protein interfaces since we think that such an understanding will pave the way to elucidate the ruleset of biomolecular recognition.

We perform our research under four themes:

For more, you check our Github Page, Dr. Karaca's Twitter account, 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)

Link to the full CV of Dr. Karaca (last update was made on 2023-12).

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)
 +9 02322994154

  1. Karaca Lab. on Computational Structural Biology

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


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


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


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


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


Hilal TAY MSc Student  hilal.tay@ibg.edu.tr


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


Buse ŞAHİN MSc Student  buse.sahin@ibg.edu.tr


Tuğçe İNAN Post-Doc Researcher  tugce.inan@ibg.edu.tr


İrem DEMİR Undergraduate Student  irem.demir@std.ibg.edu.tr


Former Members

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


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


Beyza KAYNARCA Research Assistant  beyza.kaynarca@ibg.edu.tr


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


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


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


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


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


Barış Can EKİM PhD Student  bariscan.ekim@msfr.ibg.edu.tr
+90 232 299 41 00 (0 (539) 384 29 26)

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


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


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


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


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


Beyza KAYNARCA Visiting Researcher  beyza.kaynarca@ibg.edu.tr


Selected Publications

Koşaca M, Yılmazbilek İ, Karaca E. PROT-ON: A structure-based detection of designer PROTein interface MutatiONs.. Frontiers in molecular biosciences. 2023 March ; 10 : 1063971. doi:10.3389/fmolb.2023.1063971. Download

Ozden B, Boopathi R, Barlas AB, Lone IN, Bednar J, Petosa C, Kale S, Hamiche A, Angelov D, Dimitrov S, Karaca E. Molecular Mechanism of Nucleosome Recognition by the Pioneer Transcription Factor Sox.. Journal of chemical information and modeling. 2023 June ; 63 (12) : 3839-3853. doi:10.1021/acs.jcim.2c01520. Download

Ozden B, Şamiloğlu E, Özsan A, Erguven M, Yükrük C, Koşaca M, Oktayoğlu M, Menteş M, Arslan N, Karakülah G, Barlas AB, Savaş B, Karaca E. Benchmarking the accuracy of structure-based binding affinity predictors on Spike-ACE2 deep mutational interaction set.. Proteins. 2023 November . doi:10.1002/prot.26645. Download

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, Cornelissen NV, Peters A, Karaca E, Rentmeister A. Enzymatic Generation of Double-Modified AdoMet Analogues and Their Application in Cascade Reactions with Different Methyltransferases.. Chembiochem : a European journal of chemical biology. 2022 December ; 23 (24) : e202200511. doi:10.1002/cbic.202200511. Download

Cingöz S, Soydemir D, Öner TÖ, Karaca E, Özden B, Kurul SH, Bayram E, University of Washington Center for Mendelian Genomics, Coe BP, Nickerson DA, Eichler EE. Novel biallelic variants affecting the OTU domain of the gene OTUD6B associate with severe intellectual disability syndrome and molecular dynamics simulations.. European journal of medical genetics. 2022 June ; 65 (6) : 104497. doi:10.1016/j.ejmg.2022.104497. Download

HIZ, AYŞE SEMRA; KILIÇ, SEVAL; BADEMCİ, GÜNEY; KARAKULAK, TÜLAY; ERDOĞAN, AYBİKE; YÜCEL, BURCU ÖZDEN; YAZICIOĞLU, ÇİĞDEM ERESEN; BAĞRIYANIK, ŞERİFE ESRA ERDAL; YİŞ, ULUÇ; TEKİN, MUSTAFA; KARAKÜLAH, GÖKHAN; EREK, EZGİ KARACA; and ÖZTÜRK, MEHMET. VARS1 Mutations Associated with Neurodevelopmental Disorder Are Located on A Short Amino Acid Stretch of The Anticodon-Binding Domain. Turkish Journal of Biology. 2022 January ; 46 (6) : 458-464. doi:10.55730/1300-0152.2631. 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 : 39

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)
 +9 02322994154