Research Interests
Research Interests
Molecular Dynamics & Enhanced Sampling Methods Development
Integrative Structural Biology Method Development
Computer Aided Drug Discovery
Applications in Protein Dynamics
Protein Dynamics Landscape Design
I am a molecular modeller with focus in usage and development of enhanced sampling molecular dynamics methods suchs as Metadynamics and Transition Path Sampling, as well as integrative structural biology methods to probe protein dynamics by incorporating experimental and model data (e.g Cryo-EM, NMR, transition rate constants, Alphafold data) into molecular simulations. My goal is to develop and apply state of the art computational tools for understanding and predicting macroscopic properties and function of biomolecules and small molecules based on their chemical constitution and dynamics that can revolutionise drug discovery and diagnostics.
M. Milanesi*, Z.F. Brotzakis*, M. Vendruscolo Transient interactions between the fuzzy coat and the cross-β core of brain-derived Aβ42 filaments.Sci. Adv.11,eadr7008, 2025. link
Z.F. Brotzakis, S. Zhang, MhD. H. Murtada, M. Vendruscolo . AlphaFold prediction of structural ensembles of disordered proteins. Nat Commun 16, 1632, 2025. link
P. Karatzas*, Z.F. Brotzakis*, H. Sarimveis. Small Molecules Targeting the Structural Dynamics of AR-V7 Partially Disordered Proteins Using Deep Ensemble Docking. J. Chem. Theory Comput. 2025 link
R. I. Horne, E. A. Andrzejewska, P. Alam*, Z. F. Brotzakis*. et al. Discovery of potent inhibitors of α-synuclein aggregation using structure-based iterative learning. Nat Chem Biol 20, 634–645, 2024. link
P.G. Bolhuis, Z.F. Brotzakis, B. Keller. Optimizing molecular potential models by imposing kinetic constraints with path reweighting J. Chem. Phys. 159, 074102, 2023. link
Z.F. Brotzakis Guide for determination of protein structural ensembles by combining cryo-EM data with metadynamics. FEBS Open Bio 13 (7), 1193, 2023. link
T. Bhardwaj, K. Gadhave, S.K. Kapuganti, P. Kumar, Z.F. Brotzakis et al. Amyloidogenic proteins in the SARS-CoV and SARS-CoV-2 proteomes. Nat Commun 14, 945, 2023. link
H. Mikolajek*, M. Weckener*, Z. F. Brotzakis*, J Huo, E.V. Dalietou, et. al. Correlation between binding affinity and the conformational entropy of nanobodies targeting the SARS-CoV-2 spike protein. PNAS, 119 (31):e2205412119, 2022. link
Z F. Brotzakis, Philip R Lindstedt, Ross J Taylor, Dillon J Rinauro, Nicholas C T Gallagher et al. A Structural Ensemble of a Tau-Microtubule Complex Reveals Regulatory Tau Phosphorylation and Acetylation Mechanisms. ACS Central Science, 7(12):1986–1995, 2021. link
Z. F. Brotzakis, T. Lohr, and M. Vendruscolo. Determination of intermediate state structures in the opening pathway of SARS-CoV-2 spike using cryo-electron microscopy. Chem. Sci., 12(26):9168–9175, 2021. link
Z F. Brotzakis, M. Vendruscolo, and P. G Bolhuis. A method of incorporating rate constants as kinetic constraints in molecular dynamics simulations. Proc. Natl. Acad. Sci. U.S.A., 118(2):e2012423118, 2021 link
Z F. Brotzakis, V. Limongelli, and M. Parrinello. Accelerating the Calculation of Protein-Ligand Binding Free Energy and Residence Times using Dynamically Optimized Collective Variables. J. Chem. Theory Comput., 15(1):743–750, 2019. link