Prof. Dr. PEMRA ÖZBEK SARICA

Yayın Ağı

Makaleler 42

1. Multi-approach study on diethylhexyl phthalate and monoethylhexyl phthalate binding to lysozyme: In silico, bioactivity and surface plasmon resonance analyses

Aydoğan Ahbab M., Taşteki̇l I., Pınar E. G., ÖZBEK SARICA P., Türkoğlu E. A.

Toxicology Letters , cilt.408, ss.54-64, 2025 (SCI-Expanded)

2. Binding Affinity and Interaction Mechanism of Chlorhexidine with Lysozyme: Insights from Surface Plasmon Resonance, Molecular Docking, and Molecular Dynamics Simulations

Çungur S., Taştekil I., ÖZBEK SARICA P., Türkoğlu E. A.

ChemistrySelect , cilt.10, sa.7, 2025 (SCI-Expanded, Scopus)

3. Antivirulence therapy: type IV pilus as a druggable target for bacterial infections

Basaran E., Avci F. G., Ozcan A., Kula C., Ben Ali Hassine S., Keskin O., et al.

Medicinal Chemistry Research , cilt.34, sa.2, ss.285-300, 2025 (SCI-Expanded, Scopus)

4. Elucidation of the Binding Interaction between β-sitosterol and Lysozyme using Molecular Docking, Molecular Dynamics and Surface Plasmon Resonance Analysis

Sayğı T. K., Pınar E. G., Taştekil I., ÖZBEK SARICA P., TOPÇU G., Türkoğlu E. A.

Chemistry and Biodiversity , cilt.22, sa.2, 2025 (SCI-Expanded, Scopus)

5. Understanding the PET micro/nanoplastics as an environmental stressor on pancreatin enzyme: leaching and binding characterization by multi-spectroscopic and molecular docking examination, and the resulting impact on Escherichia coli

Saygin H., Baysal A., Tilkili B., Apaydin E., ÖZBEK SARICA P.

Nanotoxicology , cilt.19, sa.5, ss.508-527, 2025 (SCI-Expanded, Scopus)

6. Attenuation of Type IV pili activity by natural products

Yalkut K., Ben Ali Hassine S., Basaran E., KULA C., Ozcan A., Avci F. G., et al.

Journal of Biomolecular Structure and Dynamics , cilt.43, sa.12, ss.5719-5729, 2025 (SCI-Expanded)

7. Surface plasmon resonance, molecular docking, and molecular dynamics simulation studies of lysozyme interaction with tannic acid

Türkoğlu E. A., Taştekil I., ÖZBEK SARICA P.

Food Science and Nutrition , cilt.12, sa.10, ss.7392-7404, 2024 (SCI-Expanded, Scopus)

8. Lung Adenocarcinoma Systems Biomarker and Drug Candidates Identified by Machine Learning, Gene Expression Data, and Integrative Bioinformatics Pipeline

Soyer S. M., ÖZBEK SARICA P., KASAVİ C.

OMICS A Journal of Integrative Biology , cilt.28, sa.8, ss.408-420, 2024 (SCI-Expanded, Scopus)

9. Polymorphism in F pocket affects peptide selection and stability of type 1 diabetes-associated HLA-B39 allotypes.

Amarajeewa A. W. P., Özcan A., Mukhtiar A., Ren X., Wang Q., Ozbek P., et al.

European journal of immunology , cilt.54, sa.6, 2024 (SCI-Expanded) Sürdürülebilir Kalkınma

10. Piperidine-based natural products targeting Type IV pili antivirulence: A computational approach

Ozcan A., Keskin O., Sariyar Akbulut B., Özbek Sarica P.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING , cilt.119, 2023 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

11. A review on the mechanistic details of OXA enzymes of ESKAPE pathogens

Avci F. G., Tastekil I., Jaisi A., ÖZBEK SARICA P., SARIYAR AKBULUT B.

PATHOGENS AND GLOBAL HEALTH , cilt.117, sa.3, ss.219-234, 2023 (SCI-Expanded, Scopus)

12. Epistatic effects between amino acid insertions and substitutions mediate toxin-resistance of vertebrate Na+, K+-ATPases

Mohammadi S., Özdemir H. I., Özbek Sarica P., Sumbul F., Stiller J., Deng Y., et al.

MOLECULAR BIOLOGY AND EVOLUTION , cilt.1, sa.1, ss.100-102, 2022 (SCI-Expanded, Scopus)

13. How Epstein-Barr virus envelope glycoprotein gp350 tricks the CR2? A molecular dynamics study

Bingöl E. N., Taştekil I., Yay C., Keskin N., ÖZBEK SARICA P.

Journal of Molecular Graphics and Modelling , cilt.114, 2022 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

14. Assessment of 13 in silico pathogenicity methods on cancer-related variants

Yazar M., ÖZBEK SARICA P.

Computers in Biology and Medicine , cilt.145, 2022 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

15. Exploring the recognition differences of peptides in TCR-pMHC complex

Bingol E. N., Özbek Sarica P.

BIOPHYSICAL JOURNAL , cilt.121, sa.3, 2022 (SCI-Expanded)

16. Systems biomarkers for papillary thyroid cancer prognosis and treatment through multi-omics networks

Gulfidan G., Soylu M., Demirel D., Erdonmez H. B. C., Beklen H., ÖZBEK SARICA P., et al.

ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS , cilt.715, 2022 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

17. Hydration modulates oxygen channel residues for oxygenation of cysteine dioxygenase: Perspectives from molecular dynamics simulations

Tariq M., Özbek Sarica P., Moin S. T.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING , cilt.110, 2022 (SCI-Expanded)

18. Differential Interactome Based Drug Repositioning Unraveled Abacavir, Exemestane, Nortriptyline Hydrochloride, and Tolcapone as Potential Therapeutics for Colorectal Cancers

beklen h., arslan s., Gulfidan G., Turanlı B., ÖZBEK SARICA P., Karademir Yılmaz B., et al.

Frontiers in Bioinformatics , cilt.1, 2021 (Hakemli Dergi) Sürdürülebilir Kalkınma

19. Unraveling the Allosteric Communication Mechanisms in T-Cell Receptor-Peptide-Loaded Major Histocompatibility Complex Dynamics Using Molecular Dynamics Simulations: An Approach Based on Dynamic Cross Correlation Maps and Residue Interaction Energy Calculations

Bingol E. N., Sercinoglu O., Özbek Sarica P.

JOURNAL OF CHEMICAL INFORMATION AND MODELING , cilt.61, sa.5, ss.2444-2453, 2021 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

20. In SilicoTools and Approaches for the Prediction of Functional and Structural Effects of Single-Nucleotide Polymorphisms on Proteins: An Expert Review

Yazar M., ÖZBEK SARICA P.

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY , cilt.25, ss.23-37, 2021 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

21. Identification of novel inhibitors of the ABC transporter BmrA

Serçinoğlu O., Senturk D., Altinisik K., Avci F., Frlan R., Tomašič T., et al.

BIOORGANIC CHEMISTRY , cilt.105, 2020 (SCI-Expanded)

22. Revisiting allostery in CREB-binding protein (CBP) using residue-based interaction energy

Yazar M., Ozbek P.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN , cilt.34, sa.9, ss.965-974, 2020 (SCI-Expanded, Scopus)

23. New Machine Learning Applications to Accelerate Personalized Medicine in Breast Cancer: Rise of the Support Vector Machines

Ozer M. E., Sarica P., ARĞA K. Y.

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY , cilt.24, sa.5, ss.241-246, 2020 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

24. Sequence-structure-function relationships in class I MHC: A local frustration perspective

Serçinoğlu O., Ozbek P.

PLOS ONE , cilt.15, sa.5, 2020 (SCI-Expanded)

25. **Computational investigation of peptide binding stabilities of HLA-B27 and HLA-B44 alleles**

Bunsuz A., SERÇİNOĞLU O., Ozbek P.

Computational Biology and Chemistry , cilt.84, 2020 (SCI-Expanded)

26. Next-Generation Sequencing Identifies BRCA1 and/or BRCA2 Mutations in Women at High Hereditary Risk for Breast Cancer with Shorter Telomere Length

Peker E., Yenmiş G., Bingöl E., Yüksel Ş., Tokat F., Özbek P., et al.

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY , cilt.24, sa.1, ss.5-15, 2020 (SCI-Expanded) Sürdürülebilir Kalkınma

27. ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism

Aydınkal R. M., Serçinoğlu O., Özbek Sarıca P.

Nucleic Acids Research , cilt.1, sa.1, 2019 (SCI-Expanded, Scopus)

28. How Do Mutations and Allosteric Inhibitors Modulate Caspase-7 Activity? A Molecular Dynamics Study

Bingol E. N., Serçinoğlu O., Özbek Sarıca P.

Journal Of Biomolecular Structure & Dynamics , cilt.37, sa.13, ss.3456-3466, 2019 (SCI-Expanded) Sürdürülebilir Kalkınma

29. HLA Moleküllerinde Peptit Ligandlarının Kompleks Stabilitesine Olan Etkisinin Araştırılması

Bunsuz A., Serçinoğlu O., Özbek Sarıca P.

International journal of advances in engineering and pure sciences (Online) , cilt.30, 2018 (Hakemli Dergi)

30. gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations

Sercinoglu O., Özbek Sarıca P.

NUCLEIC ACIDS RESEARCH , cilt.46, 2018 (SCI-Expanded)

31. HLA Proteinlerinin GNM Metodu ile Dinamik Karakterizasyonu

SERÇİNOĞLU O., ÖZBEK SARICA P.

Dokuz Eylül Üniversitesi Mühendislik Fakültesi Fen ve Mühendislik Dergisi , cilt.20, sa.59, ss.376-399, 2018 (Hakemli Dergi)

32. Computational characterization of residue couplings and micropolymorphism-induced changes in the dynamics of two differentially disease-associated human MHC class-I alleles

Sercinoglu O., Özbek Sarıca P.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS , cilt.36, ss.724-740, 2018 (SCI-Expanded) Sürdürülebilir Kalkınma

33. A computational docking study on the pH dependence of peptide binding to HLA-B27 sub-types differentially associated with ankylosing spondylitis

Sercinoglu O., Ozcan G., Kabas Z. K., ÖZBEK SARICA P.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN , cilt.30, sa.7, ss.569-581, 2016 (SCI-Expanded)

34. **Dynamic characterization of HLA-B*44 Alleles: A comparative molecular dynamics simulation study**

ÖZBEK SARICA P.

COMPUTATIONAL BIOLOGY AND CHEMISTRY , cilt.62, ss.12-16, 2016 (SCI-Expanded) Sürdürülebilir Kalkınma

35. DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex's Dynamics

Soner S., ÖZBEK SARICA P., Garzon J. I., Ben-Tal N., HALİLOĞLU T.

PLOS COMPUTATIONAL BIOLOGY , cilt.11, sa.10, 2015 (SCI-Expanded)

36. Hot Spots in a Network of Functional Sites

ÖZBEK SARICA P., Soner S., HALİLOĞLU T.

PLOS ONE , cilt.8, sa.9, 2013 (SCI-Expanded, Scopus)

37. Community wide assessment of protein interface modeling suggests improvements to design methodology

Sarel J F., Timothy A W., Strauch E., Corn J. E., Qin S., Zhou H., et al.

Journal Of Molecular Biology , cilt.414, ss.289-302, 2011 (SCI-Expanded)

38. DNABINDPROT fluctuation based predictor of DNA binding residues within a network of interacting residues

Özbek Sarıca P., Soner S., Erman B., Haliloglu T.

Nucleic Acids Research , cilt.38, ss.417-423, 2010 (SCI-Expanded)

39. Protein dynamics

ÖZBEK SARICA P., Haliloglu T.

Sigma Mühendislik ve Fen Bilimleri Dergisi , cilt.27, ss.161-170, 2009 (Hakemli Dergi)

40. Fracture mechanics analysis of arc shaped specimens for pipe grade polymers

ÖZBEK SARICA P., Argyrakis C., Leevers P.

Polymer Testing , cilt.28, ss.357-361, 2009 (SCI-Expanded)

41. Uniaxial tensile properties underlying plane stress rapid fracture resistance in polyethylene

ÖZBEK SARICA P., Leevers P.

Polymer Engineering And Science , cilt.48, ss.1855-1861, 2008 (SCI-Expanded)

42. Plane stress rapid fracture resistance of pipe grade PE Estimation from tensile drawing data

ÖZBEK SARICA P., Leevers P. S.

ANTEC Conference Proceedings , cilt.5, ss.2880-2884, 2007 (Hakemli Dergi)

Hakemli Bilimsel Toplantılarda Yayımlanmış Bildiriler 59

1. Implications of Machine Learning Approaches in Cancer for Biomarker Discovery: Oversampling and Feature Selection

Soyer S. M., Özbek Sarica P., Kasavi C.

5th International Eurasian Conference on Science, Engineering and Technology (EurasianSciEnTech 2024), Ankara, Türkiye, 26 - 28 Haziran 2024, (Özet Bildiri) Sürdürülebilir Kalkınma

2. A drug repurposing study on the inhibition of type IV pili

Özcan A., Ben Ali Hassine S., KULA C., AVCI F. G., ÖZBEK SARICA P., SARIYAR AKBULUT B.

47th FEBS Congress, Tours, Fransa, 08 Temmuz 2023, (Özet Bildiri)

3. Screening of FDA-Approved Natural Drugs as Anti-Virulence Agents Against Pseudomonas aeruginosa and Neisseria meningitidis

Özcan Yöner A., KULA C., AVCI F. G., KESKİN ÖZKAYA Z. Ö., ÖZBEK SARICA P., SARIYAR AKBULUT B.

FEMS Conference on Microbiology, Belgrade, Sırbistan, 30 Haziran 2022, (Özet Bildiri)

4. Differential Interactome Based Drug Repositioning Unraveled Potential Therapeutics for Colorectal Cancers

BEKLEN H., Arslan S., GULFİDAN G., TURANLI B., ÖZBEK SARICA P., YILMAZ B., et al.

3rd EURASIA BIOCHEMICAL APPROACHES & TECHNOLOGIES (EBAT) CONGRESS, Antalya, Türkiye, 4 - 07 Kasım 2021, (Özet Bildiri)

5. New inhibitors of the BmrA pump identified through virtual screening

Senturk D., SERÇİNOĞLU O., ALTINIŞIK KAYA F. E., Frlan R., Tomasic T., AVCI F. G., et al.

MuTaLig COST ACTION CA15135 4th WG meeting, 05 Mart 2020, (Özet Bildiri)

6. Exploring dynamics of pMHCusing accelerated molecular dynamics

Bingol E. N., ÖZBEK SARICA P.

7th International Bahçeşehir University (BAU) Drug Design Congress, 19 - 21 Aralık 2019, (Özet Bildiri)

7. Identification of allostery in CREB-Binding Protein via using pairwiseresidue interaction energy method

YAZAR M., ÖZBEK SARICA P.

7th International Bahçeşehir University (BAU) Drug Design Congress, 19 - 21 Aralık 2019, (Özet Bildiri)

8. A Tool for Investigating Protein Signaling Network by Perturbation of External Energy Dissipation

özer m. e., özdemir h. i., SERÇİNOĞLU O., Bingol E. N., ÖZBEK SARICA P.

7th International Bahçeşehir University (BAU) Drug Design Congress, 19 - 21 Aralık 2019, (Özet Bildiri)

9. Ailesel Meme Kanseri Hastalarında BRCA1 ve BRCA2 Genlerinin Yeni Nesil Dizileme Yöntemi ile Dizilenmesi ve Telomer Uzunluğuyla İlişkisi

PEKER EYÜBOĞLU İ., YENMİŞ G., BİNGÖL E. N., YÜKSEL KILIÇTURGAY Ş., TOKAT F., ÖZBEK SARICA P., et al.

Tıbbi Biyoloji ve Genetik kongresi, Türkiye, 27 - 30 Ekim 2019, (Özet Bildiri) Sürdürülebilir Kalkınma

10. Determination Of Candidate Biomarkers Through Differential Interactome in Colorectal Adenocarcinoma

BEKLEN H., GULFİDAN G., TURANLI B., ÖZBEK SARICA P., YILMAZ B., ARĞA K. Y.

The 12th International Symposium on Health Informatics and Bioinformatics (HIBIT 2019), İzmir, Türkiye, 17 - 19 Ekim 2019, (Özet Bildiri)

11. Comparative dynamical characterization of TCR and MHC molecules upon binding via molecular dynamics simulations

Bingol E. N., SERÇİNOĞLU O., ÖZBEK SARICA P.

ECOMB, 19 - 21 Eylül 2019, (Özet Bildiri)

12. Protein Networks: Development of a web tool to analyze protein structural topology

aydınkal r. m., SERÇİNOĞLU O., ÖZBEK SARICA P.

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

13. Dynamical characterization of TCRpMHC complex: A comparative molecular dynamics study

Bingol E. N., SERÇİNOĞLU O., ÖZBEK SARICA P.

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

14. Comparison of allosteric pathway identification of CREB-binding protein using computational methods

YAZAR M., ÖZBEK SARICA P.

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

15. Comparative Analysis of Two Binding Sites on The BmrA Efflux Pump

şentürk karagöz d., SERÇİNOĞLU O., ÖZBEK SARICA P., orelle c., Jault J., SARIYAR AKBULUT B.

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

16. Biophysical Links Between Polymorphism, Stability and Peptide-Binding in the Major Histocompatibility Complex

SERÇİNOĞLU O., ÖZBEK SARICA P.

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

17. VIRTUAL SCREENING FOR INHIBITORS OF THE BmrA PUMP

şentürk karagöz d., SERÇİNOĞLU O., SARIYAR AKBULUT B., ÖZBEK SARICA P., orelle c., jault j. m.

HIBIT 2018 11TH INTERNATIONAL SYMPOSIUM ON HEALTH INFORMATICS AND BIOINFORMATICS, 25 - 27 Ekim 2018, (Özet Bildiri)