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 in to our calculations, which we obtain through our collaborations.

Lately, we have been concentrated on (i) understanding the molecular basis of a number of nucleic acid modifications, (ii) developing therapeutics to inhibit over-activation of  tyrosine kinases in cancer and (iii) exploring the structural principles of epigenetic modifications.

Selected Publications

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

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 Feb ; 112 309-357. doi:10.1016/bs.apcsb.2018.01.007.

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 Mar ; 173 (1): 208-220.e220. doi:10.1016/j.cell.2018.02.032.

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


Karaca Lab. on Computational Structural Biology

Group Leader

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