We
are applying computational chemistry methods to biological systems in
our research group. Our inter-disciplinary research focuses on protein engineering and analyses of their structural/functional dynamics, ligand- and structure-based drug design, high throughput virtual screening,
machine learning, text mining, investigation of molecular mechanisms of protein/drug, protein/protein and protein/DNA interactions and optimizations protocols for rational
drug design. For this aim, together with applications of molecular
modeling tools such as homology modeling, 3D-QSAR (quantitative
structure-activity relationships), molecular docking, molecular dynamics
(MD) simulations combined with post-processing analyses (using MM/PB(GB)SA
as well as direct evaluation of Free Energy Perturbation (FEP) with
constraining schemes, and Potential of Mean Force (PMF) computations),
cheminformatics, Monte-Carlo simulations, loop modeling, de novo drug design, ADME/Tox; we are also developing programing codes for several biological problems.
Principal Investigator (PI)
of the group, Prof. Durdagi published two books on computer-aided drug
design in 2020 ("Supramolecules in Drug Design and Drug Delivery: Methods and Protocols", published by Springer and in 2010 (“Recent Advances in Computational Drug Design Studies:
The Application of In Silico Methodologies
for Bioactive Cannabinoid and Fullerene Derivatives” by VDM-Verlag).
Prof. Durdagi is the author/co-author of seven book chapters (such as
“Medicinal Chemistry Research Progress”, published by Nova Science and
"Highlights in Computational Chemistry II” published by Springer) and around 180 research articles in top peer-reviewed medicinal chemistry,
computational chemistry, quantum chemistry, bioinformatics, structural
biology, bioorganic chemistry, biophysics and computational biology
journals (i.e. Molecular Therapy; Structure; Biophysical Journal; Journal of Medicinal Chemistry; Molecular Pharmaceutics; ACS Chemical Neuroscience; Journal of
Biological Chemistry; Cellular and Molecular Life Sciences; Cancer Research; Eur. Journal of Medicinal Chemistry; Journal of Chemical Information and Modeling; Journal of Pharmacology and Experimental Therapeutics (JPET); BBA-Biomembranes; ChemMedChem; Frontiers in Chemistry; Journal of Computer-Aided Molecular Design; Current Opinion in Structural Biology; Int. Journal of Quantum Chemistry; Proteins; Chemical Physics
Letters; Channels; Journal of Enzyme Inhibition and Medicinal Chemistry, New Journal of Chemistry, etc.) with h-index of 38.
(The total citations of Prof. Durdagi's research articles are more than 4000)
Prof. Durdagi has also international patents such from World Intellectual Property Organization (WIPO), European Patent Office (EPO) and US Patent and Trademark Office (USPTO):
WO2019004970
EP3612188
US20210147421
Prof.
Durdagi’s research group currently works at the Department of Biophysics, School of Medicine, Bahcesehir University (BAU). The group of Dr Durdagi works on several
projects for better understanding the drug-receptor and protein-protein, protein-DNA interactions of different systems using several computational modeling
approaches and designing novel therapeutic compounds.
Prof. Durdagi received many prestigious national and international awards including: 
