Immunoinformatics

2025
Recent Advancements in Computational Approaches for Tailoring Toll-like Receptors and Antimicrobial Peptides Against Candida Infections
Biçer, M., Serçinoğlu, O., Okur, T.
Celal Bayar University Journal of Science, Volume 21, Issue 3, Pages 1-9
2025
Understanding Allosteric Stabilization of pMHC by Peptide Ligands Through Molecular Dynamics Simulations
Serçinoğlu, O.
Turkish Journal of Immunology, Volume 13, Issue 3, Pages 132-145
2025
Computational Prediction of Immune Epitopes
Atak, E., Eke, T. E., Serçinoğlu, O.
Encyclopedia of Bioinformatics and Computational Biology (Second Edition), Pages 690-703
2024
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., Garstka, M. A. G., Serçinoğlu, O.
Eur. J. Immunol.
2021
Unraveling the Allosteric Communication Mechanisms in T-Cell Receptor–Peptide-Loaded Major Histocompatibility Complex Dynamics Using Molecular Dynamics Simulations
Bingöl, E. N., Serçinoğlu, O., Ozbek, P.
J. Chem. Inf. Model.
2020
Sequence-structure-function relationships in class I MHC: A local frustration perspective
Serçinoğlu, O., Ozbek, P.
PLoS One
2020
Computational investigation of peptide binding stabilities of HLA-B27 and HLA-B44 alleles
Bunsuz, A., Serçinoğlu, O., Ozbek, P.
Comput. Biol. Chem.
2017
Computational characterization of residue couplings and micropolymorphism-induced changes in the dynamics of two differentially disease-associated human MHC class-I alleles
Serçinoğlu, O., Ozbek, P.
J. Biomol. Struct. Dyn.
2016
A computational docking study on the pH dependence of peptide binding to HLA-B27 sub-types differentially associated with ankylosing spondylitis
Serçinoğlu, O., Özcan, G., Kutlu Kabaş, Z., Ozbek, P.
J. Comput. Aided Mol. Des.

Drug Discovery

2025
Repurposing existing drugs to discover allosteric inhibitors of ERK5
Turhal, G., Serçinoğlu, O., Demiroglu-Zergeroglu, A.
FEBS Open Bio, Volume 15, Page 317
2025
Molecular Dynamics Simulations in Drug Discovery
Serçinoğlu, O., Wezen, X. C., Fatima, A.
Encyclopedia of Bioinformatics and Computational Biology (Second Edition), Volume 6, Pages 645-656
2024
Drug Repurposing and Multi-Target Therapies
Şahin, Ş., Önel, Ö., Kızılay, E. B., Serçinoğlu, O.
Encyclopedia of Bioinformatics and Computational Biology (Second Edition)
2024
Unraveling the ligand specificity and promiscuity of the Staphylococcus aureus NorA efflux pump: a computational study
Işık, E. B., Serçinoğlu, O.
J. Biomol. Struct. Dyn.
2024
In Vitro, In Vivo, and In Silico Analysis of Pyraclostrobin and Cyprodinil and Their Mixture Reveal New Targets and Signaling Mechanisms
Kim, Y., Bereketoglu, C., Serçinoğlu, O., Pradhan, A.
Chem. Res. Toxicol.
2021
In silico and in vitro assessment of androgen receptor antagonists
Serçinoğlu, O., Bereketoglu, C., Olsson P. E., Pradhan, A.
Comput. Biol. Chem.
2020
Identification of novel inhibitors of the ABC transporter BmrA
Serçinoğlu, O., Senturk, D., Altinisik Kaya, F. E., Avci, F. G., Frlan, R., Tomašič, T., Ozbek, P., Orelle, C., Jault, JM., Sarıyar Akbulut, B.
Bioorganic Chemistry
2019
In Silico Databases and Tools for Drug Repurposing
Serçinoğlu, O., Ozbek, P.
In Silico Drug Design: Repurposing Techniques and Methodologies, Pages 649-677
2022
Computational approaches used in Anticancer plants
Ulucan-Karnak, F., Yilmaz-Sercinoglu, Z., Sercinoglu, O., Ali, A.
Plant-Derived Anticancer Drugs in OMICS Era: Biosynthesis, Function and Applications, Apple Academic Press

Protein Engineering

2026
A novel Amycolatopsis sulphurea L-alanine dehydrogenase with enhanced bidirectional catalysis: Rational design, expression, and biochemical characterization
Aksu, T. O., Serçinoğlu, O., Aktaş, F., Binay, B.
International Journal of Biological Macromolecules
2025
Computational Protein Engineering
Okur, T., Serçinoğlu, O.
Encyclopedia of Bioinformatics and Computational Biology (Second Edition), Volume 6, Pages 159-171

Software & Tools

2018
gRINN: A tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations
Serçinoğlu, O., Ozbek, P.
Nucleic Acids Res.
2019
ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism
Aydınkal, R. M., Serçinoğlu, O., Ozbek, P.
Nucleic Acids Res.

Computational Biology

2022
Non-apoptotic cell death induction via sapogenin based supramolecular particles
Üner, G., Bedir, E., Serçinoğlu, O., Ballar Kırmızıbayrak, P.
Scientific Reports
2019
How do mutations and allosteric inhibitors modulate caspase-7 activity? A molecular dynamics study
Bingöl, E. N., Serçinoğlu, O., Ozbek, P.
J. Biomol. Struct. Dyn.