Peer-reviewed articles
Journal of Molecular Graphics and Modelling 114, 108196, (2022)
Assessment of 13 in silico pathogenicity methods on cancer-related variants. Computers in Biology and Medicine, (2022),105434,ISSN 0010-4825.doi:10.1016/j.compbiomed.2022.105434
Gulfidan, G., Soylu, M., Demirel, D., Erdonmez, H. B. C., Beklen, H., Sarica, P. O., ... & Turanli, B. Systems biomarkers for papillary thyroid cancer prognosis and treatment through multi-omics networks. Archives of Biochemistry and Biophysics (2022): 109085. doi:10.1016/j.abb.2021.109085
Tariq, Muhammad; OZBEK, Pemra; MOIN, Syed Tarique. Hydration modulates oxygen channel residues for oxygenation of cysteine dioxygenase: Perspectives from molecular dynamics simulations. Journal of molecular graphics & modelling, 110: 108060.(2022) doi: 10.1016/j.jmgm.2021.108060
Bingöl, E. N., Serçinoğlu, O. & Ozbek, P. 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. J. Chem. Inf. Model. acs.jcim.1c00338 (2021) doi:10.1021/acs.jcim.1c00338.
Yazar, M., Ozbek, P. In Silico Tools and Approaches for the Prediction of Functional and Structural Effects of Single-Nucleotide Polymorphisms on Proteins: An Expert Review. OMICS: A Journal of Integrative Biology. Oct 2020. https://doi.org/10.1089/omi.2020.0141
Serçinoğlu, O., & Ozbek, P. Sequence-structure-function relationships in class I MHC: A local frustration perspective. PloS one, 2020. 15(5), e0232849. https://doi.org/10.1371/journal.pone.0232849
OMICS: A Journal of Integrative Biology.May 2020.241-246.http://doi.org/10.1089/omi.2020.0001
OMICS: A Journal of Integrative Biology.Jan 2020.5-15.http://doi.org/10.1089/omi.2019.0103
Bunsuz, A., Serçinoğlu, O., & Ozbek, P. Computational investigation of peptide binding stabilities of HLA-B*27 and HLA-B*44 alleles. Computational Biology and Chemistry, 84, 107195, 2020. https://doi.org/10.1016/j.compbiolchem.2019.107195
Serçinoğlu, O., & Ozbek, P. Sequence-structure-function relationships in class I MHC: a local frustration perspective. BioRxiv, 867473. 2019. https://doi.org/10.1101/867473
Aydınkal RM, Serçinoğlu O., Ozbek P., ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism, Nucleic Acids Research, 2019, https://doi.org/10.1093/nar/gkz390
Bingol EN., Sercinoglu O., Ozbek P., How Do Mutations and Allosteric Inhibitors Modulate Caspase-7 Activity? A Molecular Dynamics Study, Journal of Biomolecular Structure and Dynamics, 2019, https://doi.org/10.1080/07391102.2018.1517611
Sercinoglu O., Ozbek P., gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations, Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W554–W562, https://doi.org/10.1093/nar/gky381
Sercinoglu O., Ozbek P., Computational characterization of residue couplings and micropolymorphism-induced changes in the dynamics of two differentially disease-associated human MHC class-I alleles, Journal of Biomolecular Structure and Dynamics, 2018. https://doi.org/10.1080/07391102.2017.1295884
Sercinoglu O., Ozcan G., Kutlu Kabas Z., Ozbek P., A computational docking study on the pH dependence of peptide binding to HLA-B27 sub-types differentially associated with ankylosing spondylitis, Journal of Computer-Aided Molecular Design, 30(7), 569-581, 2016. https://doi.org/10.1007/s10822-016-9934-z
Ozbek P., Dynamic characterization of HLA-B*44 Alleles: A comparative molecular dynamics simulation study, Computational Biology and Chemistry, 62(12-16), 2016. https://doi.org/10.1016/j.compbiolchem.2016.02.019
Soner S., Ozbek P., Garzon, JI., Ben-Tal, N., Haliloglu, T., DynaFace: Discrimination between Obligatory and Non-obligatory ProteinProtein Interactions Based on the Complex’s Dynamics, PLoS Comput Biol 11(10): e1004461. 2015, https://doi.org/10.1371/ journal.pcbi.1004461
Ozbek P., Soner, S., Haliloglu, T., Hot Spots in a network of functional sites, PLOS ONE 8(9), e74320, 2013. https://doi.org/10.1371/journal.pone.0074320
Fleishman S. et al. (Group 13: Soner,S. Ovali, S.K., Ozbek, P.,Ben Tal, N., Haliloglu, T.), Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology, Journal of Molecular Biology, 414 (2):289-302, 2011. https://doi.org/10.1016/j.jmb.2011.09.031
Ozbek, P., Soner S., Erman B., Haliloglu, T., DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues, Nucleic Acids Research, Web Server issue, 38:W417-423, 2010. https://doi.org/10.1093/nar/gkq396
Ozbek, P., Haliloglu, T., Protein Dynamics, Sigma: Journal of Engineering and Natural Sciences, 27:161-170, 2009
Book Chapter
Bingol, E.N., Serçinoğlu, O., Ozbek Sarica, P. PROTEİN: YAPISI, MÜHENDİSLİĞİ, ETKİLEŞİMLERİ, DİNAMİĞİ VE İLAÇ TASARIMINDAKİ YERİ. In Saliha Ece Acuner, editors, In Silico Drug Design, Ankara Nobel Tıp Kitabevleri, 2021
Serçinoğlu, O., Ozbek Sarica, P. In Silico Databases and Tools for Drug Repurposing. In Kunal Roy, editors, In Silico Drug Design, Elsevier, 2019 February
National Publications
Bunsuz, A., Sercinoglu O., Ozbek P., HLA Moleküllerinde Peptit Ligandlarının Kompleks Stabilitesine Olan Etkisinin Araştırılması, Marmara Fen Bilimleri Dergisi, Cilt 4, 2018.
Sercinoglu O., Ozbek, P., HLA Proteinlerinin GNM Metodu ile Dinamik Karakterizasyonu, Dokuz Eylül Üniversitesi-Mühendislik Fakültesi Fen ve Mühendislik Dergisi, Cilt 20, Sayı 59, Mayıs, 2018, doi: 10.21205/deufmd. 2018205931
Conference Papers, Oral Presentations and Posters
Aslıhan Özcan, Kerem Yalkut, Berna Sarıyar Akbulut, Pemra Özbek, Computational approach for inhibition of ATPases Acting Antagonistically in Type IV Pilus in Neisseria meningitidis by FDA-approved natural drugs, 8th International Bahçeşehir University (BAU) Drug Design Congress, 15 December 2022
Ilgaz Taştekil, Fatma Gizem Avci, Berna Sariyar Akbulut, Pemra Ozbek Sarica, Investigation of OXA enzyme inhibitors using computational tools, 8th International Bahçeşehir University (BAU) Drug Design Congress, 15 December 2022
Metin Yazar, Pemra Ozbek, Pathogenicity prediction of cancer-related variants with protein sequence, structure, dynamics-based features, 8th International Bahçeşehir University (BAU) Drug Design Congress, 15 December 2022
Aslihan Ozcan, Ceyda Kula, Fatma Gizem Avcı, Ozlem Keskin Ozkaya, Berna Sariyar Akbulut, Pemra Ozbek Sarica., Screening of FDA-Approved Natural Drugs as Anti-Virulence Agents Against Pseudomonas aeruginosa and Neisseria meningitidis FEMS Conference on Microbiology in Belgrade, 30 Haziran – 2 Temmuz 2022.
Peshala Amarajeewa, Aslıhan Özcan, Pemra Özbek Sarıca, Malgorzata A. Garstka, Onur Serçinoğlu., Comparative evaluation of binding affinities of peptide ligands to HLA-B alleles differentially-associated with Type 1 Diabetes Mellitus (T1DM), 5th International Symposium on Bioinformatics, 15-17 Aralık 2021.
Yazar M., Özbek P. (2021, Eylül). Comparison of the performance of in silico pathogenicity prediction tools on cancer-related variants. HIBIT 2021.
Özer ME.,Özbek P., Arga KY. Support Vector Machine supported by Disease Ontology (SVM-DO) to identify mRNA signatures discriminating tumour cells. HIBIT Eylül 2021.
Aslihan Ozcan, Halil Ibrahim Ozdemir, Ozlem Keskin Ozkaya, Berna Sariyar Akbulut, Pemra Ozbek Sarica., Investigation of type 4 pili protein's inhibition mechanism and discovery of corresponding natural inhibitory drugs, The 13th International Symposium On Health Informatics and Bioinformatics (HIBIT), 22-23 Ekim 2020.
Özer M. E. , Özdemir H.İ. , SERÇİNOĞLU O., Bingol E. N. , ÖZBEK SARICA P., A Tool for Investigating Protein Signaling Network by Perturbation of External Energy Dissipation, 7th International Bahçeşehir University (BAU) Drug Design Congress, 19 - 21 Aralık 2019
YAZAR M., ÖZBEK SARICA P., Identification of allostery in CREB-Binding Protein via using pairwiseresidue interaction energy method, 7th International Bahçeşehir University (BAU) Drug Design Congress, 19 - 21 Aralık 2019
Bingol E. N. , ÖZBEK SARICA P., Exploring dynamics of pMHCusing accelerated molecular dynamics, 7th International Bahçeşehir University (BAU) Drug Design Congress, 19 - 21 Aralık 2019
Bingol E. N. , SERÇİNOĞLU O., ÖZBEK SARICA P. Dynamical characterization of TCRpMHC complex: A comparative molecular dynamics study, 6th International BAU-Drug Design Congress, 13 - 15 Aralık 2018
SERÇİNOĞLU O., ÖZBEK SARICA P., Biophysical Links Between Polymorphism, Stability and Peptide-Binding in the Major Histocompatibility Complex, 6th International BAU-Drug Design Congress, 13 - 15 Aralık 2018
Şentürk Karagöz D., SERÇİNOĞLU O., ÖZBEK SARICA P. , orelle c., Jault J., SARIYAR AKBULUT B., Comparative Analysis of Two Binding Sites on The BmrA Efflux Pump, 6th International BAU-Drug Design Congress, Türkiye, 13 - 15 Aralık 2018
YAZAR M., ÖZBEK SARICA P., Comparison of allosteric pathway identification of CREB-binding protein using computational methods, 6th International BAU-Drug Design Congress, 13 - 15 Aralık 2018
Aydınkal R.M.. , SERÇİNOĞLU O., ÖZBEK SARICA P.Protein Networks: Development of a web tool to analyze protein structural topology, 6th International BAU-Drug Design Congress, 13 - 15 Aralık 2018
Şentürk Karagöz D., SERÇİNOĞLU O., SARIYAR AKBULUT B. , ÖZBEK SARICA P. , orelle c., jault j. m., VIRTUAL SCREENING FOR INHIBITORS OF THE BmrA PUMP, HIBIT 2018 11TH INTERNATIONAL SYMPOSIUM ON HEALTH INFORMATICS AND BIOINFORMATICS, 25 - 27 Ekim 2018
Yazar M., Sercinoglu, O., Ozbek, P., Comparison of computational allosteric pathwayidentification methods, International conference on applied mathematics, modeling and Life Sciences, Istanbul, Turkey, 3-10 October 2018.
Aydınkal RM., Sercinoglu, O., Ozbek, P., Development of a web-based tool for network analysis of protein structures, International conference on applied mathematics, modeling and Life Sciences, Istanbul, Turkey, 3-10 October 2018.
Bingol EN., Sercinoglu, O., Ozbek, P., Investigation of catalytic loop motions and global dynamics ofcaspase- 7 structures, International conference on applied mathematics, modeling and Life Sciences, Istanbul, Turkey, 3-10 October 2018.
Bunsuz A., Sercinoglu, O., Ozbek, P., Computational Approaches to the Investigation ofPeptide-MHC Complex Stability, International conference on applied mathematics, modeling and Life Sciences, Istanbul, Turkey, 3-10 October 2018.
Ozbek, P., Understanding the dynamic natureof proteins using molecular dynamics (MD)simulations, International conference on applied mathematics, modeling and Life Sciences, Istanbul, Turkey, 3-10 October 2018, (Oral Presentation).
Sercinoglu, O., Ozbek, P., Biophysical basis of MHC Class I polymorphism, International conference on applied mathematics, modeling and Life Sciences, Istanbul, Turkey, 3-10 October 2018, (Oral Presentation).
Sercinoglu, O., Ozbek, P., Quantifying Peptide Binding Affinities from Non-equilibrium Work, 62nd Biophysical Society Annual Meeting, San Francisco, USA, 17-21 February 2018.
Sercinoglu, O., Ozbek, P, A Software Tool for Parallel Computation and Characterization of Residue Interaction Energies from Molecular Dynamics Simulations, International Symposium on Chemistry via Computation Applications on Molecular Nanoscience, Istanbul,Turkey, 30 October 2017.
Bunsuz, A., Sercinoglu, O., Ozbek, P, effect of temperature on the molecular dynamics simulations of HLA-A*02 alleles, International Symposium on Chemistry via Computation Applications on Molecular Nanoscience, Istanbul,Turkey, 30 October 2017.
Bingol, EN., Sercinoglu, O., Ozbek, P, Construction of allosteric residue networks in caspase-7 using energy perturbation responses, International Symposium on Chemistry via Computation Applications on Molecular Nanoscience, Istanbul,Turkey, 30 October 2017.
Sercinoglu, O., Ozbek, P, Steered Molecular Dynamics Simulation for Efficient Ranking of Peptide - MHC Class I Binding Affinities, 5th International BAU-Drug Design Congress, İstanbul, Turkey, 19-21 October 2017, (Poster&Oral Presentation).
Bunsuz, A., Sercinoglu, O., Ozbek, P, Immunogenic Peptide - HLA-A*02:01 Complexes Studied by Comparative Molecular Dynamics Simulation, 5th International BAU-Drug Design Congress, İstanbul, Turkey, 19-21 October 2017.
Bingol, EN., Sercinoglu, O., Ozbek, P, Detection of the allosteric residue network in effector caspase molecules by energy dissipation model, 5th International BAU-Drug Design Congress, İstanbul, Turkey, 19-21 October 2017.
Bunsuz, A., Sercinoglu, O., Ozbek, P, Investigation of peptide binding affinity and thermal stability of Human Leukocyte Antigens (HLAs), 19th IUPAB and 11th EBSA Congress, Edinburgh, UK, 16-20 July 2017.
Sercinoglu, O., Ozbek, P, Allelic dependence of MHC-I stability on peptide termini contacts in MD simulations, 19th IUPAB and 11th EBSA Congress, Edinburgh, UK, 16-20 July 2017.
Bunsuz, A., Sercinoglu, O., Ozbek, P, Investigation of peptide binding affinity and complex stability of Human Leukocyte Antigens (HLAs), 4th International BAU-Drug Design Congress, İstanbul, Turkey, 12-15 October 2016.
Bingol, EN., Sercinoglu, O., Ozbek, P, Searching a communication pathway between allosteric site and binding region in effector caspase molecules, 4th International BAU-Drug Design Congress, İstanbul, Turkey, 12-15 October 2016..
Sercinoglu, O., Ozbek, P, Allelic Modulation of Global Dynamics of HLA-B*27:05 and HLA-B*27:09 Molecules, 13.Greta Pifat Mrzljak Uluslararası Biyofizik Yaz Okulu, Hırvatistan, 01-10 September 2016.
Bunsuz, A., Sercinoglu, O., Ozbek, P, HLA-B*44 Alellerinin Peptid Bağlanma Davranış Mekanizmalarının Hesaplamalı Olarak araştırılması, Biruni Üniversitesi Bilgisayar Destekli İlaç Tasarımı, İstanbul, Türkiye, 16-17 Mayıs 2016 (poster ödülü).
Bingol, E.N., Sercinoglu, O., Ozbek, P, Investigating Dynamics of HLA Molecules By Energy Dissipation, 60th Biophysical Society Meeting, Los Angeles, USA, February 27-March 2, 2016.
Kutlu Kabas, Z., Ozcan, G., Sercinoglu, O., Ozbek, P, Investigation of the Binding Behaviour of HLA-B27 Alleles at varying pH Conditions Using Computational Methods, 3rd International BAU-Drug Design Congress, Istanbul, Turkey, October 1-3, 2015.
Bunsuz A., Sercinoglu, O., Ozbek, P., Computational Study on the Binding Behaviour of HLA-B44 Alleles, 3rd International BAU-Drug Design Congress, Istanbul, Turkey, October 1-3, 2015.
Bingol, EN., Sercinoglu, O., Ozbek, P., Computational Investigation of Protein Dynamics Based On Energy Dissipation, 3rd International BAU-Drug Design Congress, Istanbul, Turkey, October 1-3, 2015.
Sercionlu, O., Ozbek, P., Structural Characterization of Peptide Binding to Class I MHC Proteins using Protein Energy Networks from Molecular Dynamics Simulations, 3rd International BAU-Drug Design Congress, Istanbul, Turkey, October 1-3, 2015.
Ozcan, G., Kutlu Kabas, Z., Sercinoglu, O., Ozbek, P., Computational Study on the Effect of pH on the Binding Behaviour of HLA-B Alleles , 10th European Biophysics Congress, Dresden, Germany, July 17-22, 2015.
Sercinoglu, O., Ozbek, P., Peptide dependent binding-stabilization effect of β2 microglobulin on HLA B27 alleles, 10th European Biophysics Congress, Dresden, Germany,July 17-22, 2015.
Ozcan, G., Kutlu Kabas, Z., Sercinoglu, O., Ozbek, P., Binding Behavior of HLA-B Alleles Related to Ankylosing Spondylitis (AS) Disease: A Comparative Study by Computational Methods, ECCB'14, the 13th European Conference on Computational Biology, Strasbourg, September 7-10, 2014.
Kutlu Kabas, Z., Ozcan, G., Sercinoglu, O., Ozbek, P., Computational Study on the Effect of pH on the Binding Behaviour of HLA-B Alleles, ECCB'14, the 13th European Conference on Computational Biology, Strasbourg, September 7-10, 2014.
Sercinoglu, O., Ozbek, P., An Investigation of the Effects of Model Simplification and Water Box Shell Size on the Molecular Dynamics Simulations of Peptide-loaded Major Histocompatibility Complex Proteins, Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations, Istanbul, Turkey, September 10-14, 2014
Ozcan, G., Sercinoglu, O., Kutlu Kabas, Z., Ozbek, P., Comparison of the Binding Behavior of HLA-B Alleles Related to Ankylosing Spondylitis Disease by Computational Methods, Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations, Istanbul, Turkey, September 10-14, 2014.
Sercinoglu, O., Ozcan, G., Ozbek, P., Computational Investigation of the Energy Exchange Pathways in Peptide-loaded Major Histocompatibility Complex Proteins, Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations, Istanbul, Turkey, September 10-14, 2014.
Kaya, C., Soner, S., Ozbek, P., Haliloglu, T., The intrinsic dynamics of partner chains aid in the detection of native complexes amongst docking decoys, Seminar Presentation, CAPRI Meeting 2013, Utrecht, Holland, 2013.
Kaya, C., Onel O., Soner, S., Ozbek, P., Haliloglu, T., Unique Scoring Function for Molecular Docking of Proteins, Poster Presentation, Imperial College Hermes, Summer School on Material Simulations, London, UK, 2012.
Soner, S., Ozbek, P., Haliloglu, T. , Dynamics define protein binding, Poster Presentation, Chemical Physics Congress-IX Izmir, Turkey, 2010.
Ozbek, P., Protein-protein and protein-DNA interactions by elastic network models, Seminar Presentation, Informatics Institute, ITU, Istanbul, Turkey, 2010.
Ozbek, P., Soner, S., Chen, N., Kalman, M., Erman, B., Ben-tal, N., Haliloglu, T. , Dynamics and evolutionary conservation of inter-protein interfaces aid in the detection of native complexes amongst docking decoys, Poster Presentation, 4th CAPRI meeting, Barcelona, Spain, 2009
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