Dr. Öğr. Üyesi EZGİ KARACA EREK

Yayın Ağı

SCI, SSCI ve AHCI İndekslerine Giren Dergilerde Yayınlanan Makaleler

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 , 2023 (SCI-Expanded)

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

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)

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 , 2023 (SCI-Expanded) Sürdürülebilir Kalkınma

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 , 2023 (SCI-Expanded) Sürdürülebilir Kalkınma

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)

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 , sa.6, 2023 (SCI-Expanded) Sürdürülebilir Kalkınma

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 , 2023 (SCI-Expanded)

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)

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)

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)

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 , 2022 (SCI-Expanded)

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 , ss.1-13, 2022 (SCI-Expanded)

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, ss.104497, 2022 (SCI-Expanded) Sürdürülebilir Kalkınma

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)

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

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)

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)

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)

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)

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

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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

Diğer Dergilerde Yayınlanan Makaleler

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 , 2021 (Hakemli Dergi)

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 , 2021 (Hakemli Dergi)

Hakemli Kongre / Sempozyum Bildiri Kitaplarında Yer Alan Yayınlar

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 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

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

A Structural Insight into DNA Methylation

Doğan D., KARACA EREK E.

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

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

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

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

Integrative Modeling of Biomolecular Interactions

KARACA EREK E.

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

Structure Determination of Molecular Machines

KARACA EREK E.

Workshop in Applied Structural Bioinformatics, Bergen, Norveç, 16 - 20 Ekim 2017

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

Upgrading HADDOCK for the Structure Calculation of Molecular Machines

KARACA EREK E.

Haddock Developer’s Meeting, Utrecht, Hollanda, 22 - 23 Ağustos 2017

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

Kitap & Kitap Bölümleri

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

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

Atıf (WoS)

1618

H-İndeks (WoS)

Atıf (Scopus)

2479

H-İndeks (Scopus)

Atıf (Scholar)

H-İndeks(Scholar)

Proje

Tez Danışmanlığı

Açık Erişim

BM Sürdürülebilir Kalkınma Amaçları

Yayınlar & Eserler

SCI, SSCI ve AHCI İndekslerine Giren Dergilerde Yayınlanan Makaleler

Diğer Dergilerde Yayınlanan Makaleler

Hakemli Kongre / Sempozyum Bildiri Kitaplarında Yer Alan Yayınlar

Kitap & Kitap Bölümleri

Metrikler

Yayın

Atıf (WoS)

H-İndeks (WoS)

Atıf (Scopus)

H-İndeks (Scopus)

Atıf (Scholar)

H-İndeks(Scholar)

Proje

Tez Danışmanlığı

Açık Erişim