Omics Computational Biophysics

Principal Investigator: Assist. Prof. Seyit KALE

Our team aims to elucidate the working mechanisms of molecular-level machines operating within the cell in both health and disease, using high-performance computational methods, molecular modeling, and statistical physics tools. Additionally, we conduct research on strategies for designing small molecules, peptides, and antibodies for therapeutic intervention to ensure these mechanisms function correctly. The pathological characterization we developed for the rare disease known as Rahman syndrome is being generalized and extended to include other rare diseases that affect our region.

Visual: Prediction of the shelf life (stability) of a monoclonal antibody produced for cancer therapy using computational tools and its optimization through single-point mutations.

Video: Atomistic simulation of the DNA-binding mechanism of the linker histone H1.4 protein in an ultra-rare Rahman syndrome patient, performed using high-performance computing tools.

PUBLICATIONS

Döşeme, H., Uluçay, T., and Kale, S. "Dynamic recognition of the nucleosome core particle by select chromatin factors." Procedia Computer Science, (2025): 130-139.

Asfa, S.S., Arshinchi Bonab, R., Önder, O., Uça Apaydın, M., Döşeme, H., Küçük, C., Georgakilas, A.G., Stadler, B.M., Logotheti, S., Kale, S. and Pavlopoulou, A., 2024. Computer-Aided Identification and Design of Ligands for Multi-Targeting Inhibition of a Molecular Acute Myeloid Leukemia Network. Cancers, 16(21), p.3607.

Kale, S., Boopathi, R., Belotti, E., Lone, I.N., Graies, M., Schröder, M., Petrova, M., Papin, C., Bednar, J., Ugrinova, I. and Hamiche, A., 2023. The CENP-A nucleosome: where and when it happens during the inner kinetochore’s assembly. Trends in Biochemical Sciences, 48(10), pp.849-859.

Arslan, M., Uluçay, T., Kale, S. and Kalyoncu, S., 2023. Engineering of conserved residues near antibody heavy chain complementary determining region 3 (HCDR3) improves both affinity and stability. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 1871(4), p.140915.

Ozden, B., Boopathi, R., Barlas, A.B., Lone, I.N., Bednar, J., Petosa, C., Kale, S., Hamiche, A., Angelov, D., Dimitrov, S. and Karaca, E., 2023. Molecular mechanism of nucleosome recognition by the pioneer transcription factor Sox. Journal of Chemical Information and Modeling, 63(12), pp.3839-3853.

PROJECTS

European Molecular Biology Organization Installation Grant, IG No 5056-2022, Identification of Epigenetic Mechanisms of Mitotic Fidelity in Chromatin. PI: Seyit Kale, €250,000, ongoing.

European High Performance Computing Joint Undertaking (EuroHPC JU), AI- and Data-intensive Computing Grant EHPC-AI-2024A01-088, Investigation of Novel Epigenetic Signals through Combinatorial Crosstalk between Histone Isoforms. PI: Seyit Kale, 32,000 node-hours (4,096,000 core-hours), completed.

European High Performance Computing Joint Undertaking (EuroHPC JU), Regular Access Call Computing Grant EHPC-REG-2023R02-125, Project RAHMAN. PI: Seyit Kale, 36,938 node-hours (4,728,064 core-hours), completed.

TÜBİTAK 1001 122Z215, Chromatin Folding Mechanism Mediated by Linker Histone H1 under Disease and Normal Conditions. PI: Dimitar Angelov, Researcher: Seyit Kale, completed.

European Union PRACE-DECI-17 (Partnership for Advanced Computing in Europe, Distributed European Computing Initiative), Computing Grant for Project EPICENTROME. PI: Seyit Kale, 24,960,000 core-hours, completed.

European Union PRACE-DECI-16, Computing Grant for Project CCAN. PI: Seyit Kale, 1,344,000 core-hours, completed.

Staff

Active Members

Serhan Turunç (PhD Student)
Gözdem Çavdar Arıcı (PhD Student)
Büşra Yüksel (MSc Student)
Büşra Boztepe (MSc Student)
Özge Öz (Intern)
Halil İbrahim Topuz (Undergraduate Student)
İdil Bilge Tunç (Undergraduate Student)

Former Members

Ceyda Nur Öksüm (Undergraduate Student)
Cem Taşkıran (Intern)
Asude Cansu (Intern)
Bora Güvendiren (Intern)
Onur Önder (MSc Student)
Merve Uça (PhD Student)
Tuğçe Uluçay (Researcher)
Deniz Doğan (Researcher)