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Ezgi Karaca - Publications

Affiliations: 
Izmir Biomedicine and Genome Center 
 Dokuz Eylul University, İzmir, Turkey 
Area:
Integrative Modeling, Bimolecular Docking, Protein-protein Interactions, Protein Dynamics
Website:
https://www.ibg.edu.tr/research-programs/groups/karaca-lab/
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31/50 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Turan G, Olgun ÇE, Ayten H, Toker P, Ashyralyyev A, Savaş B, Karaca E, Muyan M. Dynamic proximity interaction profiling suggests that YPEL2 is involved in cellular stress surveillance. Protein Science : a Publication of the Protein Society. e4859. PMID 38145972 DOI: 10.1002/pro.4859  0.762
2023 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. PMID 37991066 DOI: 10.1002/prot.26645  0.72
2023 Kryshtafovych A, Montelione GT, Rigden DJ, Mesdaghi S, Karaca E, Moult J. Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15. Proteins. PMID 37872703 DOI: 10.1002/prot.26584  0.32
2023 Ozden B, Kryshtafovych A, Karaca E. The impact of AI-based modeling on the accuracy of protein assembly prediction: Insights from CASP15. Proteins. PMID 37861057 DOI: 10.1002/prot.26598  0.722
2023 Ozden B, Kryshtafovych A, Karaca E. The Impact of AI-Based Modeling on the Accuracy of Protein Assembly Prediction: Insights from CASP15. Biorxiv : the Preprint Server For Biology. PMID 37503072 DOI: 10.1101/2023.07.10.548341  0.724
2023 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. 63: 3839-3853. PMID 37307148 DOI: 10.1021/acs.jcim.2c01520  0.731
2023 Özden-Yılmaz G, Savas B, Bursalı A, Eray A, Arıbaş A, Senturk S, Karaca E, Karakülah G, Erkek-Ozhan S. Differential Occupancy and Regulatory Interactions of KDM6A in Bladder Cell Lines. Cells. 12. PMID 36980177 DOI: 10.3390/cells12060836  0.755
2022 Hiz S, Kiliç S, Bademci G, Karakulak T, Erdoğan A, Özden B, Eresen Ç, Erdal E, Yiş U, Tekin M, Karakülah G, Karaca E, Öztürk M. mutations associated with neurodevelopmental disorder are located on a short amino acid stretch of the anticodon-binding domain. Turkish Journal of Biology = Turk Biyoloji Dergisi. 46: 458-464. PMID 37529793 DOI: 10.55730/1300-0152.2631  0.65
2022 Cingoz S, Soydemir D, Oner TO, Karaca E, Ozden B, Kurul SH, Bayram E, 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. 104497. PMID 35430327 DOI: 10.1016/j.ejmg.2022.104497  0.65
2021 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. PMID 34796993 DOI: 10.1002/prot.26284  0.772
2021 Ozden B, Kryshtafovych A, Karaca E. Assessment of the CASP14 Assembly Predictions. Proteins. PMID 34337786 DOI: 10.1002/prot.26199  0.738
2019 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, et al. Correction to: Novel mutations in KMT2B offer pathophysiological insights on childhood-onset progressive dystonia. Journal of Human Genetics. PMID 31388109 DOI: 10.1038/S10038-019-0644-Y  0.308
2019 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, et al. Novel mutations in KMT2B offer pathophysiological insights into childhood-onset progressive dystonia. Journal of Human Genetics. PMID 31165786 DOI: 10.1038/S10038-019-0625-1  0.303
2018 Bonvin AMJJ, Karaca E, Kastritis PL, Rodrigues JPGLM. Defining distance restraints in HADDOCK. Nature Protocols. PMID 29942005 DOI: 10.1038/S41596-018-0017-6  0.581
2017 Karaca E, Rodrigues JPGLM, Graziadei A, Bonvin AMJJ, Carlomagno T. M3: an integrative framework for structure determination of molecular machines. Nature Methods. PMID 28805795 DOI: 10.1038/Nmeth.4392  0.566
2017 Vangone A, Rodrigues JPGLM, Xue LC, van Zundert GCP, Geng C, Kurkcuoglu Z, Nellen M, Narasimhan S, Karaca E, van Dijk M, Melquiond ASJ, Visscher KM, Trellet M, Kastritis PL, Bonvin AMJJ. Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI (page 418). Proteins. 85: 1589-1590. PMID 28730688 DOI: 10.1002/Prot.25339  0.755
2016 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. 5. PMID 28009253 DOI: 10.7554/Elife.19706  0.347
2016 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 Round1. Proteins. PMID 27802573 DOI: 10.1002/Prot.25198  0.757
2016 Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, ... ... Karaca E, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. PMID 27122118 DOI: 10.1002/Prot.25007  0.797
2015 van Zundert GC, Rodrigues JP, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond AS, van Dijk M, de Vries SJ, Bonvin AM. The HADDOCK2.2 web server: User-friendly integrative modeling of biomolecular complexes. Journal of Molecular Biology. PMID 26410586 DOI: 10.1016/J.Jmb.2015.09.014  0.755
2015 Rodrigues JP, Karaca E, Bonvin AM. Information-driven structural modelling of protein-protein interactions. Methods in Molecular Biology (Clifton, N.J.). 1215: 399-424. PMID 25330973 DOI: 10.1007/978-1-4939-1465-4_18  0.737
2014 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, et al. Blind prediction of interfacial water positions in CAPRI. Proteins. 82: 620-32. PMID 24155158 DOI: 10.1002/Prot.24439  0.782
2013 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. 81: 2119-28. PMID 23913867 DOI: 10.1002/Prot.24382  0.774
2013 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. 69: 683-94. PMID 23633577 DOI: 10.1107/S0907444913007063  0.601
2013 Karaca E, Bonvin AM. Advances in integrative modeling of biomolecular complexes. Methods (San Diego, Calif.). 59: 372-81. PMID 23267861 DOI: 10.1016/J.Ymeth.2012.12.004  0.603
2012 Rodrigues JP, Trellet M, Schmitz C, Kastritis P, Karaca E, Melquiond AS, Bonvin AM. Clustering biomolecular complexes by residue contacts similarity. Proteins. 80: 1810-7. PMID 22489062 DOI: 10.1002/Prot.24078  0.74
2012 Melquiond ASJ, Karaca E, Kastritis PL, Bonvin AMJJ. Next challenges in protein-protein docking: From proteome to interactome and beyond Wiley Interdisciplinary Reviews: Computational Molecular Science. 2: 642-651. DOI: 10.1002/Wcms.91  0.701
2011 Karaca E, Bonvin AM. A multidomain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes. Structure (London, England : 1993). 19: 555-65. PMID 21481778 DOI: 10.1016/J.Str.2011.01.014  0.623
2010 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. 5: e12430. PMID 20865150 DOI: 10.1371/Journal.Pone.0012430  0.572
2010 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. 78: 3242-9. PMID 20718048 DOI: 10.1002/Prot.22814  0.805
2010 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 & Cellular Proteomics : McP. 9: 1784-94. PMID 20305088 DOI: 10.1074/Mcp.M000051-Mcp201  0.81
Low-probability matches (unlikely to be authored by this person)
2021 Karakulak T, Rifaioglu AS, Rodrigues JPGLM, Karaca E. Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl. Frontiers in Molecular Biosciences. 8: 658906. PMID 34195226 DOI: 10.3389/fmolb.2021.658906  0.299
2010 Tozluoğlu M, Karaca E, Nussinov R, Haliloğlu T. A mechanistic view of the role of E3 in sumoylation. Plos Computational Biology. 6. PMID 20865051 DOI: 10.1371/Journal.Pcbi.1000913  0.294
2018 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. PMID 29551265 DOI: 10.1016/J.Cell.2018.02.032  0.294
2022 Karaca E, Prévost C, Sacquin-Mora S. Modeling the Dynamics of Protein-Protein Interfaces, How and Why? Molecules (Basel, Switzerland). 27. PMID 35335203 DOI: 10.3390/molecules27061841  0.293
2016 Bebel A, Karaca E, Kumar B, Stark WM, Barabas O. Author response: Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending Elife. DOI: 10.7554/Elife.19706.028  0.278
2008 Tozluoğlu M, Karaca E, Haliloglu T, Nussinov R. Cataloging and organizing p73 interactions in cell cycle arrest and apoptosis. Nucleic Acids Research. 36: 5033-49. PMID 18660513 DOI: 10.1093/Nar/Gkn481  0.26
2019 Pavlopoulou A, Karaca E, Balestrazzi A, Georgakilas AG. Phylogenetic and Structural Analyses of Plant Endogenous Danger Signaling Molecules upon Stress. Oxidative Medicine and Cellular Longevity. 2019: 8683054. PMID 31396307 DOI: 10.1155/2019/8683054  0.257
2019 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. 7: 281. PMID 31803740 DOI: 10.3389/Fcell.2019.00281  0.253
2021 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. 6: 1254-1265. PMID 33490784 DOI: 10.1021/acsomega.0c04672  0.252
2018 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. 112: 309-357. PMID 29680240 DOI: 10.1016/Bs.Apcsb.2018.01.007  0.248
2011 Karaca E, Tozluoğlu M, Nussinov R, Haliloğlu T. Alternative allosteric mechanisms can regulate the substrate and E2 in SUMO conjugation. Journal of Molecular Biology. 406: 620-30. PMID 21216249 DOI: 10.1016/J.Jmb.2010.12.044  0.24
2023 Koşaca M, Yılmazbilek İ, Karaca E. PROT-ON: A structure-based detection of designer PROTein interface MutatiONs. Frontiers in Molecular Biosciences. 10: 1063971. PMID 36936988 DOI: 10.3389/fmolb.2023.1063971  0.223
2021 Gungor S, Oktay Y, Hiz S, Aranguren-Ibáñez Á, Kalafatcilar I, Yaramis A, Karaca E, Yis U, Sonmezler E, Ekinci B, Aslan M, Yilmaz E, Özgör B, Balaraju S, Szabo N, et al. Autosomal recessive variants in alter the γ-tubulin ring complex leading to neurodevelopmental disease. Iscience. 24: 101948. PMID 33458610 DOI: 10.1016/j.isci.2020.101948  0.216
2023 Atalay N, Akcan EK, Gül M, Ayan E, Destan E, Ertem FB, Tokay N, Çakilkaya B, Nergiz Z, Karakadioğlu G, Kepceoğlu A, Yapici İ, Tosun B, Baldir N, Yildirim G, ... ... Karaca E, et al. Cryogenic X-ray crystallographic studies of biomacromolecules at Turkish Light Source "". Turkish Journal of Biology = Turk Biyoloji Dergisi. 47: 1-13. PMID 37529114 DOI: 10.55730/1300-0152.2637  0.153
2023 Gul M, Ayan E, Destan E, Johnson JA, Shafiei A, Kepceoğlu A, Yilmaz M, Ertem FB, Yapici İ, Tosun B, Baldir N, Tokay N, Nergiz Z, Karakadioğlu G, Paydos SS, ... ... Karaca E, et al. Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source. Scientific Reports. 13: 8123. PMID 37208392 DOI: 10.1038/s41598-023-33989-0  0.143
2022 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. PMID 36288101 DOI: 10.1002/cbic.202200511  0.138
2022 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 & Dynamics. 1-13. PMID 36270968 DOI: 10.1080/07391102.2022.2131627  0.112
2020 Demirel E, Karaca E, Yuksel Durmaz Y. Effective PEGylation method to improve biocompatibility of graphene derivatives European Polymer Journal. 124: 109504. DOI: 10.1016/j.eurpolymj.2020.109504  0.049
2023 Dioken DN, Ozgul I, Yilmazbilek I, Yakicier MC, Karaca E, Erson-Bensan AE. An alternatively spliced PD-L1 isoform PD-L1∆3, and PD-L2 expression in breast cancers: implications for eligibility scoring and immunotherapy response. Cancer Immunology, Immunotherapy : Cii. 72: 4065-4075. PMID 37768345 DOI: 10.1007/s00262-023-03543-y  0.041
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