Dr. Öğr. Üyesi EZGİ KARACA EREK

Yayın Ağı

Makaleler 53

1. So close yet so far apart: distinct flanking sequence recognition by DNMT3A and DNMT3B

Barlas A. B., KARACA EREK E.

Communications Biology , cilt.8, sa.1, 2025 (SCI-Expanded)

2. E2-regulated transcriptome complexity revealed by long-read direct RNA sequencing: from isoform discovery to truncated proteins

DÖKEN D. N., ÖZGÜL İ., Yilmazbilek I., Almeric E., Eroglu I. C., Cicek M., et al.

RNA biology , cilt.22, sa.1, ss.1-21, 2025 (SCI-Expanded)

3. An NADH-controlled gatekeeper of ATP synthase

Schildhauer F., Ryl P. S., Lauer S. M., Lenz S., Barlas A. B., Ouzounidis V. R., et al.

Molecular Cell , cilt.85, sa.13, ss.2567, 2025 (SCI-Expanded)

4. Towards a Greener AlphaFold2 Protocol for Antibody–Antigen Modeling: Insights From CAPRI Round 55

Savaş B., Yılmazbilek İ., Özsan A., KARACA EREK E.

Proteins: Structure, Function and Bioinformatics , 2025 (SCI-Expanded)

5. The HADDOCK2.4 web server for integrative modeling of biomolecular complexes

Honorato R. V., Trellet M. E., Jimenez-Garcia B., Schaarschmidt J. J., Giulini M., Reys V., et al.

NATURE PROTOCOLS , cilt.19, sa.11, 2024 (SCI-Expanded) Sürdürülebilir Kalkınma

6. Benchmarking the accuracy of structure-based binding affinity predictors on Spike–ACE2 deep mutational interaction set

Ozden B., Şamiloğlu E., Özsan A., Erguven M., Yükrük C., Koşaca M., et al.

Proteins: Structure, Function and Bioinformatics , cilt.92, sa.4, ss.529-539, 2024 (SCI-Expanded) Sürdürülebilir Kalkınma

7. Dynamic proximity interaction profiling suggests that YPEL2 is involved in cellular stress surveillance.

Turan G., Olgun Ç. E., Ayten H., Toker P., Ashyralyyev A., Savaş B., et al.

Protein science : a publication of the Protein Society , cilt.33, 2024 (SCI-Expanded)

8. An alternatively spliced PD-L1 isoform PD-L1∆3, and PD-L2 expression in breast cancers: implications for eligibility scoring and immunotherapy response

DÖKEN D. N., ÖZGÜL İ., Yilmazbilek I., Yakicier M. C., KARACA EREK E., ERSON BENSAN A. E.

Cancer Immunology, Immunotherapy , cilt.72, sa.12, ss.4065-4075, 2023 (SCI-Expanded) Sürdürülebilir Kalkınma

9. The impact of AI-based modeling on the accuracy of protein assembly prediction: Insights from CASP15

Ozden B., Kryshtafovych A., KARACA EREK E.

Proteins: Structure, Function and Bioinformatics , cilt.91, sa.12, ss.1636-1657, 2023 (SCI-Expanded)

10. Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15

Kryshtafovych A., Montelione G. T., Rigden D. J., Mesdaghi S., Karaca Erek E., Moult J.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , cilt.91, sa.12, ss.1903-1911, 2023 (SCI-Expanded) Sürdürülebilir Kalkınma

11. Genetic complementation screening and molecular docking give new insight on phosphorylation-dependent Mastl kinase activation.

Erguven M., Kilic S., Karaca E., Diril M. K.

Journal of biomolecular structure & dynamics , cilt.41, ss.1-13, 2023 (SCI-Expanded)

12. Molecular Mechanism of Nucleosome Recognition by the Pioneer Transcription Factor Sox

Ozden B., Boopathi R., Barlas A. B., Lone I. N., Bednar J., Petosa C., et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING , cilt.63, sa.12, ss.3839-3853, 2023 (SCI-Expanded) Sürdürülebilir Kalkınma

13. Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source

Gul M., Ayan E., Destan E., Johnson J. A., Shafiei A., Kepceoğlu A., et al.

Scientific reports , cilt.13, sa.1, ss.8123, 2023 (SCI-Expanded)

14. Differential Occupancy and Regulatory Interactions of KDM6A in Bladder Cell Lines

Özden-Yılmaz G., Savas B., Bursalı A., Eray A., Arıbaş A., ŞENTÜRK Ş., et al.

CELLS , cilt.12, sa.6, 2023 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

15. Cryogenic X-ray crystallographic studies of biomacromolecules at Turkish Light Source “Turkish DeLight”

Atalay N., Akcan E. K., Gül M., Ayan E., Destan E., Ertem F. B., et al.

Turkish Journal of Biology , cilt.47, sa.1, 2023 (SCI-Expanded)

16. PROT-ON: A structure-based detection of designer PROTein interface MutatiONs

Koşaca M., Yılmazbilek İ., Karaca E.

Frontiers in Molecular Biosciences , cilt.10, 2023 (SCI-Expanded)

17. Enzymatic Generation of Double-Modified AdoMet Analogues and Their Application in Cascade Reactions with Different Methyltransferases

Erguven M., Cornelissen N. V., Peters A., KARACA EREK E., Rentmeister A.

CHEMBIOCHEM , cilt.23, 2022 (SCI-Expanded)

18. Novel biallelic variants affecting the OTU domain of the gene OTUD6B associate with severe intellectual disability syndrome and molecular dynamics simulations

Cingöz S., Soydemir D., Öner T. Ö., Karaca E., Özden B., Kurul S. H., et al.

European Journal of Medical Genetics , cilt.65, sa.6, 2022 (SCI-Expanded) Sürdürülebilir Kalkınma

19. A C-term truncated EIF2B gamma protein encoded by an intronically polyadenylated isoform introduces unfavorable EIF2B gamma-EIF2 gamma interactions

ÇIRÇIR HATIL A., KÖKSAL BIÇAKCI G., Savas B., DÖKEN D. N., Henden S. O., CAN T., et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , cilt.90, sa.3, ss.889-897, 2022 (SCI-Expanded) Sürdürülebilir Kalkınma

20. Modeling the Dynamics of Protein-Protein Interfaces, How and Why?

Karaca E., Prevost C., Sacquin-Mora S.

MOLECULES , cilt.27, sa.6, 2022 (SCI-Expanded)

21. VARS1 mutations associated with neurodevelopmental disorder are located on a short amino acid stretch of the anticodon-binding domain

Hız A. S., Kılıç S., Bademci G., Karakulak T., Erdogan A., Ozden B., et al.

Turkish Journal of Biology , cilt.46, sa.6, ss.458-464, 2022 (SCI-Expanded, Scopus, TRDizin) Sürdürülebilir Kalkınma

22. Assessment of the CASP14 assembly predictions

Ozden B., Kryshtafovych A., KARACA EREK E.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , cilt.89, sa.12, ss.1787-1799, 2021 (SCI-Expanded)

23. Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl

Karakulak T., RİFAİOĞLU A. S., Rodrigues J. P. G. L. M., Karaca E.

FRONTIERS IN MOLECULAR BIOSCIENCES , cilt.8, 2021 (SCI-Expanded)

24. Türk Ulusal Bilim e-Altyapısı TRUBA'da Moleküler Dinamik Paketi GROMACS'in Performans Optimizasyonu

SAVAŞ B., KARACA EREK E.

International Journal of Advances in Engineering and Pure Sciences , cilt.33, ss.609-613, 2021 (Hakemli Dergi)

25. Arayüz Mutasyonlarının Protein Etkileşimlerine Tesirini Tahmin Eden Algoritmalarla HADDOCK'un Performansının Karşılaştırılması

Koşaca M., Şamiloğlu E., KARACA EREK E.

International Journal of Advances in Engineering and Pure Sciences , cilt.33, ss.592-608, 2021 (Hakemli Dergi)

26. How Far Are We from the Rapid Prediction of Drug Resistance Arising Due to Kinase Mutations?

Erguven M., Karakulak T., Diril M. K., KARACA EREK E.

ACS OMEGA , cilt.6, sa.2, ss.1254-1265, 2021 (SCI-Expanded)

27. **Autosomal recessive variants in TUBGCP2 alter the γ-tubulin ring complex leading to neurodevelopmental disease**

GÜNGÖR S., OKTAY Y., Hiz S., Aranguren-Ibanez A., Kalafatcilar I., Yaramis A., et al.

ISCIENCE , cilt.24, sa.1, 2021 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

28. Effective PEGylation method to improve biocompatibility of graphene derivatives

Demirel E., KARACA EREK E., YÜKSEL DURMAZ Y.

EUROPEAN POLYMER JOURNAL , cilt.124, 2020 (SCI-Expanded)

29. More Favorable Palmitic Acid Over Palmitoleic Acid Modification of Wnt3 Ensures Its Localization and Activity in Plasma Membrane Domains

Azbazdar Y., Ozalp O., Sezgin E., Veerapathiran S., Duncan A. L., Sansom M. S. P., et al.

FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY , cilt.7, 2019 (SCI-Expanded)

30. Novel mutations in KMT2B offer pathophysiological insights into childhood-onset progressive dystonia

Dafsari H. S., Sprute R., Wunderlich G., Daimagueler H., KARACA EREK E., Contreras A., et al.

JOURNAL OF HUMAN GENETICS , cilt.64, sa.8, ss.803-813, 2019 (SCI-Expanded)

31. In Silico Phylogenetic and Structural Analyses of Plant Endogenous Danger Signaling Molecules upon Stress.

Pavlopoulou A., KARACA EREK E., Balestrazzi A., Georgakilas A. G.

Oxidative medicine and cellular longevity , cilt.2019, ss.8683054, 2019 (SCI-Expanded) Sürdürülebilir Kalkınma

32. Defining distance restraints in HADDOCK

Bonvin A. M. J. J., KARACA EREK E., Kastritis P. L., Rodrigues J. P. G. L. M.

NATURE PROTOCOLS , cilt.13, sa.7, ss.1503, 2018 (SCI-Expanded)

33. Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance

Rubio-Cosials A., Schulz E. C., Lambertsen L., Smyshlyaev G., Rojas-Cordova C., Forslund K., et al.

CELL , cilt.173, sa.1, ss.208-240, 2018 (SCI-Expanded)

34. Peptide Derivatives of Erythropoietin in the Treatment of Neuroinflammation and Neurodegeneration

Ercan I., Tufekci K. U., Karaca E., GENÇ Ş., Genc K.

THERAPEUTIC PROTEINS AND PEPTIDES , cilt.112, ss.309-357, 2018 (SCI-Expanded) Sürdürülebilir Kalkınma

35. M3: an integrative framework for structure determination of molecular machines

KARACA EREK E., Rodrigues J. P. G. L. M., Graziadei A., Bonvin A. M. J. J., Carlomagno T.

NATURE METHODS , cilt.14, sa.9, ss.897-905, 2017 (SCI-Expanded)

36. Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1

Vangone A., Rodrigues J. P. G. L. M., Xue L. C., van Zundert G. C. P., Geng C., Kurkcuoglu Z., et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , cilt.85, sa.3, ss.417-423, 2017 (SCI-Expanded)

37. Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending

Bebel A., KARACA EREK E., Kumar B., Stark W. M., Barabas O.

ELIFE , cilt.5, 2016 (SCI-Expanded)

38. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Lensink M. F., Velankar S., Kryshtafovych A., Huang S., Schneidman-Duhovny D., Sali A., et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , cilt.84, ss.323-348, 2016 (SCI-Expanded)

39. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

van Zundert G. C. P., Rodrigues J. P. G. L. M., Trellet M., Schmitz C., Kastritis P. L., KARACA EREK E., et al.

JOURNAL OF MOLECULAR BIOLOGY , cilt.428, sa.4, ss.720-725, 2016 (SCI-Expanded)

40. Information-Driven Structural Modelling of Protein-Protein Interactions

Rodrigues J. P. G. L. M., KARACA EREK E., Bonvin A. M. J. J.

MOLECULAR MODELING OF PROTEINS: 2ND EDITION , cilt.1215, ss.399-424, 2015 (SCI-Expanded) Sürdürülebilir Kalkınma

41. Blind prediction of interfacial water positions in CAPRI

Lensink M. F., Moal I. H., Bates P. A., Kastritis P. L., Melquiond A. S. J., KARACA EREK E., et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , cilt.82, sa.4, ss.620-632, 2014 (SCI-Expanded)

42. Defining the limits of homology modeling in information-driven protein docking

Rodrigues J. P. G. L. M., Melquiond A. S. J., KARACA EREK E., Trellet M., van Dijk M., van Zundert G. C. P., et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , cilt.81, sa.12, ss.2119-2128, 2013 (SCI-Expanded)

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

KARACA EREK E., Bonvin A. M. J. J.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY , cilt.69, ss.683-694, 2013 (SCI-Expanded) Sürdürülebilir Kalkınma

44. Advances in integrative modeling of biomolecular complexes

KARACA EREK E., Bonvin A. M. J. J.

METHODS , cilt.59, sa.3, ss.372-381, 2013 (SCI-Expanded)

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

Melquiond A. S. J., KARACA EREK E., Kastritis P. L., Bonvin A. M. J. J.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE , cilt.2, sa.4, ss.642-651, 2012 (SCI-Expanded)

46. Clustering biomolecular complexes by residue contacts similarity

Rodrigues J. P. G. L. M., Trellet M., Schmitz C., Kastritis P., KARACA EREK E., Melquiond A. S. J., et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , cilt.80, sa.7, ss.1810-1817, 2012 (SCI-Expanded)

47. A Multidomain Flexible Docking Approach to Deal with Large Conformational Changes in the Modeling of Biomolecular Complexes

KARACA EREK E., Bonvin A. M. J. J.

STRUCTURE , cilt.19, sa.4, ss.555-565, 2011 (SCI-Expanded)

48. Alternative Allosteric Mechanisms Can Regulate the Substrate and E2 in SUMO Conjugation

KARACA EREK E., Tozluoglu M., Nussinov R., HALİLOĞLU T.

JOURNAL OF MOLECULAR BIOLOGY , cilt.406, sa.4, ss.620-630, 2011 (SCI-Expanded)

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

de Vries S. J., Melquiond A. S. J., Kastritis P. L., KARACA EREK E., Bordogna A., van Dijk M., et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , cilt.78, sa.15, ss.3242-3249, 2010 (SCI-Expanded)

50. Understanding the Role of the Josephin Domain in the PolyUb Binding and Cleavage Properties of Ataxin-3

Nicastro G., Todi S. V., KARACA EREK E., Bonvin A. M. J. J., Paulson H. L., Pastore A.

PLOS ONE , cilt.5, sa.8, 2010 (SCI-Expanded)

51. Building Macromolecular Assemblies by Information-driven Docking

KARACA EREK E., Melquiond A. S. J., de Vries S. J., Kastritis P. L., Bonvin A. M. J. J.

MOLECULAR & CELLULAR PROTEOMICS , cilt.9, sa.8, ss.1784-1794, 2010 (SCI-Expanded)

52. A Mechanistic View of the Role of E3 in Sumoylation

Tozluoglu M., KARACA EREK E., Nussinov R., Halilogiu T.

PLOS COMPUTATIONAL BIOLOGY , cilt.6, sa.8, 2010 (SCI-Expanded)

53. Cataloging and organizing p73 interactions in cell cycle arrest and apoptosis

Tozluoglu M., KARACA EREK E., HALİLOĞLU T., Nussinov R.

NUCLEIC ACIDS RESEARCH , cilt.36, sa.15, ss.5033-5049, 2008 (SCI-Expanded) Sürdürülebilir Kalkınma

Hakemli Bilimsel Toplantılarda Yayımlanmış Bildiriler 14

1. Investigation of the Effects of Mutations in the FYR Module of Kabuki Syndrome-Associated KMT2D Gene on Protein Interactions and Chromatin Organization

Özden Yılmaz G., Yılmazbilek İ., Ölmez Türker A., Ozkan Kucuk N. E., ÖZLÜ SICAKKAN N., KARAKÜLAH G., et al.

9th International Congress of the Molecular Biology Association of Turkey, İzmir, Türkiye, 12 - 14 Eylül 2024, (Özet Bildiri)

2. KDM6A shows distinct profiles in bladder

Özden Yılmaz G., Savaş B., Bursalı A., Eray A., Arıbaş A., Şentürk Ş., et al.

1st Epigenetics Society International Meeting “Epigenetics of Disease and Development”, Rome, İtalya, 12 - 14 Ekim 2023, ss.209-210, (Özet Bildiri)

3. Integrative modelling with HADDOCK - https://meetings.embo.org/event/19-integrative-structural-biology

Bonvin A. M., KARACA EREK E.

Practical integrative structural biology, Hamburg, Almanya, 3 - 09 Ekim 2019, (Tam Metin Bildiri)

4. TAM FAMILY PROTEIN AXL’s LIGAND SELECTIVITY IS REGULATED BY THREE CHARGED AMINO ACIDS

Karakulak T., Batur T., Rodrigues J. P., Öztürk M., KARACA EREK E.

ISMB/ECCB 2019, Basel, İsviçre, 21 - 25 Temmuz 2019, (Özet Bildiri)

5. Towards characterizing the factors tuning the specificity of biomolecular complexes

KARACA EREK E.

6th International BAU Drug Design Congress, İstanbul, Türkiye, 13 - 15 Aralık 2018, (Özet Bildiri)

6. Molecular specificity of TAM family receptorstowards different ligands

Karakulak T., KARACA EREK E.

11th International Symposium onHealth Informatics and Bioinformatics, Antalya, Türkiye, 25 - 27 Ekim 2018, (Özet Bildiri)

7. A Structural Insight into DNA Methylation

Doğan D., KARACA EREK E.

11th International Symposium onHealth Informatics and Bioinformatics, Antalya, Türkiye, 25 - 27 Ekim 2018, (Özet Bildiri)

8. Investigating Sequence Specificity in Mammalian De novo DNA Methyltransferases through Structural Insight

Doğan D., KARACA EREK E.

6thInternational Congress of theMolecular Biology Associationof Turkey, İzmir, Türkiye, 5 - 08 Eylül 2018, (Özet Bildiri)

9. Analysis of Mitotic Functions of Mastl Kinase

erguven m., Karakulak T., KARACA EREK E., Diril M. K.

6thInternational Congress of theMolecular Biology Associationof Turkey, İzmir, Türkiye, 5 - 08 Eylül 2018, (Özet Bildiri)

10. Integrative Modeling of Biomolecular Interactions

KARACA EREK E.

6thInternational Congress of theMolecular Biology Associationof Turkey, İzmir, Türkiye, 5 - 08 Eylül 2018, (Özet Bildiri)

11. Structure Determination of Molecular Machines

KARACA EREK E.

Workshop in Applied Structural Bioinformatics, Bergen, Norveç, 16 - 20 Ekim 2017, (Özet Bildiri)

12. Regulation of c-Met signaling by Neddylation in HCC cells

Yılmaz Y., güloglu b., Topel H., KARACA EREK E., ATABEY S. N.

42.FEBS Cogress fom molecules to cell and back, 7 - 10 Eylül 2017, cilt.284, ss.262, (Özet Bildiri)

13. Upgrading HADDOCK for the Structure Calculation of Molecular Machines

KARACA EREK E.

Haddock Developer’s Meeting, Utrecht, Hollanda, 22 - 23 Ağustos 2017, (Özet Bildiri)

14. An Integrative Framework for Structure Determination of Molecular Machines

KARACA EREK E., Rodrigues J. P., Andrea G., Bonvin A. M., Carlomagno T.

10th International Symposium on Health Informatics and Bioinformatics, Girne, Kıbrıs (Kktc), 28 - 30 Haziran 2017, (Özet Bildiri)

Kitaplar 2

1. Protein Etkileşimlerinin Deneysel ve Hesaplamalı Yaklaşımlarla Bütüncül Olarak Modellenmesi

ACUNER S. E., İmat N. B., İlter M., Şamiloğlu E., KARACA EREK E., ŞENSOY Ö.

PROTEİN: Yapısı, mühendisliği, etkileşimleri, dinamiği ve ilaç tasarımındaki yeri, Dr. Öğretim Üyesi Saliha Ece ACUNER, Editör, Ankara Nobel Tıp Kitabevleri, Ankara, ss.223-237, 2022

2. Peptide derivatives of erythropoietin in the treatment of neuroinflammation and neurodegeneration

ERCAN İ., TÜFEKCİ K. U., KARACA EREK E., GENÇ Ş., GENÇ K. K.

Therapeutic Proteins and Peptides (Advances in protein chemistry and structural biology, Volume 112), ROSSEN DONEV, Editör, Academic Press , ss.309-357, 2018

Metrikler

Yayın

Yayın (WoS)

Yayın (Scopus)

Atıf (WoS)

3446

H-İndeks (WoS)

Atıf (Scopus)

3545

H-İndeks (Scopus)

Atıf (Scholar)

4955

H-İndeks (Scholar)

Atıf (Sobiad)

H-İndeks (Sobiad)

Proje

Tez Danışmanlığı

Açık Erişim

BM Sürdürülebilir Kalkınma Amaçları

Yayınlar & Eserler

Yayın

Yayın (WoS)

Yayın (Scopus)

Atıf (WoS)

H-İndeks (WoS)

Atıf (Scopus)

H-İndeks (Scopus)

Atıf (Scholar)

H-İndeks (Scholar)

Atıf (Sobiad)

H-İndeks (Sobiad)

Proje

Tez Danışmanlığı

Açık Erişim