Molecular Modeling & Drug Design Laboratory
Dr. Suleyman Selim CINAROGLU's Lab
Web Page: https://cinaroglulab.github.io/
Laboratory Description:
The Molecular Modeling & Drug Design Laboratory focuses on developing computational approaches for drug discovery and molecular-level investigation of biological systems. Our laboratory integrates computational chemistry, molecular modeling, artificial intelligence (AI), and biophysics to explore biomolecular interactions and to support the rational design of novel therapeutic compounds.
Research Topics:
-
Molecular Modeling & Simulations
We employ molecular dynamics (MD) simulations, molecular docking, and free energy calculations to investigate biomolecular behavior at the atomic level. -
Computer-Aided Drug Discovery (CADD)
Structure-based and ligand-based approaches are used to develop computational pipelines for hit identification and lead optimization, accelerating the drug discovery process. -
AI-Driven Drug Design
Machine learning and AI-based models are integrated to improve docking protocols, predict bioactive molecules, and enhance the efficiency of virtual screening workflows. -
Multiscale Simulations
Quantum, atomistic, and coarse-grained simulation techniques are combined to study protein–ligand and protein–nanomaterial interactions, facilitating the design of novel biomaterials and therapeutic strategies. -
Host–Guest Chemistry & Thermodynamic Calculations
We develop datasets and computational methodologies to predict binding affinities and molecular recognition patterns, providing insights into non-covalent interactions relevant to rational drug design.
Selected publications:
Çınaroğlu, S.S. & Biggin, P.C. (2023) J. Chem. Inf. Model. 63, 6095–6108.
Çınaroğlu, S.S. & Biggin, P.C. (2023) Chemical Science 14, 6792–6805.
Gorgulla et al. (2023) bioRxiv, 2023-04.
Çınaroğlu, S.S. & Timuçin, E. (2020) Briefings in Bioinformatics 21, 2112–2125.
Çınaroğlu, S.S. & Biggin, P.C. (2021) J. Phys. Chem. B 125, 1558–1567.
Gorgulla et al. (2021) Int. J. Mol. Sci. 22, 5807.
Çınaroğlu, S.S. & Timuçin, E. (2019) J. Chem. Inf. Model. 59, 3846–3859.
