Biyomühendislik Ana Bilim Dalı Tez Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/417

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Browsing Biyomühendislik Ana Bilim Dalı Tez Koleksiyonu by Author "İlmek, Özkan"

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    Identification of single domain antibodies against SARS-CoV-2 omicron variant via protein-protein docking approaches
    (Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2022) İlmek, Özkan; AGÜ, Fen Bilimleri Enstitüsü, Biyomühendislik Ana Bilim Dalı
    Omicron, became the dominant variant in 2022 in terms of spreading rate, has managed to evade from an immune system of patients due to its unique mutations. Single domain antibodies (sdAb) which are functionally important parts of conventional antibodies are commonly used for diagnosis and treatment. Although there are many sdAbs developed to combat coronavirus in recent years, their effectiveness against Omicron variant has not been sufficiently tested and the effect of mutations regarding neutralization level is not clear. In this study, structure modelling of 850 sdAb sequences obtained from previous studies were generated using AlphaFold 2 and effectiveness of these sdAbs against Omicron variant was tested via protein-protein docking approach. In the docking process, within a realistic approach, missing residues were completed into Spike protein PDB structures, and Spike protein homotrimer structure in closed state conformation was used. Finally, top 1000 and top 100 scores are determined as a threshold value for different protein-protein docking scoring functions such as HDOCK, PRODIGY and Bluues. sdAbs that have successful results for Omicron variant were listed. There were 4 sdAbs which exceed the threshold values after 2 different docking experiments against the Omicron variant. The scripting codes and methodological approach developed within this thesis can be used against new SARS-CoV-2 variants that may emerge in the future or other diseases.