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Z. F. Brotzakis · SciRah

Researcher profile · Semantic Scholar

Z. F. Brotzakis

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Z. F. Brotzakis — researcher profile on SciRah

h-index: 19
Works: 59
Citations: 997

Most-cited papers

AlphaFold prediction of structural ensembles of disordered proteins
Z. F. Brotzakis, Sheng-Yu Zhang, M. Murtada, M. Vendruscolo
2023bioRxiv125 citations Open access
Semantic Scholar
Folding a small protein using harmonic linear discriminant analysis.
Dan Mendels, GiovanniMaria Piccini, Z. F. Brotzakis, Y. Yang +1 more
2018Journal of Chemical Physics67 citations Open access
Semantic Scholar
Accelerating the Calculation of Protein-Ligand Binding Free Energy and Residence Times using Dynamically Optimized Collective Variables
Z. F. Brotzakis, V. Limongelli, M. Parrinello
2018bioRxiv66 citations Open access
Semantic Scholar
A Structural Ensemble of a Tau-Microtubule Complex Reveals Regulatory Tau Phosphorylation and Acetylation Mechanisms
Z. F. Brotzakis, P. R. Lindstedt, Ross J Taylor, Dillon J. Rinauro +3 more
2020bioRxiv60 citations Open access
Semantic Scholar
Discovery of potent inhibitors of α-synuclein aggregation using structure-based iterative learning
Robert I. Horne, Ewa A. Andrzejewska, P. Alam, Z. F. Brotzakis +12 more
2021bioRxiv49 citations Open access
Semantic Scholar
Amyloidogenic proteins in the SARS-CoV and SARS-CoV-2 proteomes
Taniya Bhardwaj, K. Gadhave, S. K. Kapuganti, Prateek Kumar +11 more
2023Nature Communications43 citations Open access
Semantic Scholar
Dynamics of Hydration Water around Native and Misfolded α-Lactalbumin.
Z. F. Brotzakis, C. C. Groot, W. H. Brandeburgo, H. J. Bakker +1 more
2016Journal of Physical Chemistry B41 citations
Semantic Scholar
Structure-Based Discovery of Small-Molecule Inhibitors of the Autocatalytic Proliferation of α-Synuclein Aggregates
Sean Chia, Z. F. Brotzakis, Robert I. Horne, A. Possenti +8 more
2021bioRxiv38 citations Open access
Semantic Scholar
Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes
H. Mikolajek, M. Weckener, Z. F. Brotzakis, J. Huo +16 more
2022Proceedings of the National Academy of Sciences of the United States of America37 citations Open access
Semantic Scholar
A method of incorporating rate constants as kinetic constraints in molecular dynamics simulations
Z. F. Brotzakis, M. Vendruscolo, P. Bolhuis
2020Proceedings of the National Academy of Sciences of the United States of America36 citations Open access
Semantic Scholar
A one-way shooting algorithm for transition path sampling of asymmetric barriers.
Z. F. Brotzakis, P. Bolhuis
2016Journal of Chemical Physics33 citations Open access
Semantic Scholar
PLUMED Tutorials: A collaborative, community-driven learning ecosystem.
G. A. Tribello, Massimiliano Bonomi, G. Bussi, Carlo Camilloni +59 more
2024Journal of Chemical Physics31 citations Open access
Semantic Scholar
Approximating free energy and committor landscapes in standard transition path sampling using virtual interface exchange.
Z. F. Brotzakis, P. Bolhuis
2019Journal of Chemical Physics28 citations Open access
Semantic Scholar
Multiplexed Digital Characterization of Misfolded Protein Oligomers via Solid-State Nanopores
Sarah E. Sandler, Robert I. Horne, Sara Rocchetti, Robert Novak +8 more
2023Journal of the American Chemical Society25 citations Open access
Semantic Scholar
Determination of the Structure and Dynamics of the Fuzzy Coat of an Amyloid Fibril of IAPP Using Cryo-Electron Microscopy
Z. F. Brotzakis, T. Löhr, Steven D. Truong, Samuel E. Hoff +2 more
2022bioRxiv25 citations Open access
Semantic Scholar
Determination of intermediate state structures in the opening pathway of SARS-CoV-2 spike using cryo-electron microscopy
Z. F. Brotzakis, T. Löhr, M. Vendruscolo
2020Chemical Science24 citations Open access
Semantic Scholar
Optimizing molecular potential models by imposing kinetic constraints with path reweighting.
P. Bolhuis, Z. F. Brotzakis, B. Keller
2023Journal of Chemical Physics22 citations Open access
Semantic Scholar
Enhanced Sampling of Protein Conformational Transitions via Dynamically Optimized Collective Variables
Z. F. Brotzakis, M. Parrinello
2018bioRxiv22 citations Open access
Semantic Scholar
Secondary Processes Dominate the Quiescent, Spontaneous Aggregation of α-Synuclein at Physiological pH with Sodium Salts
Robert I. Horne, Michael A. Metrick, Wing K. Man, Dillon J. Rinauro +4 more
2023ACS Chemical Neuroscience20 citations Open access
Semantic Scholar
Water structure and dynamics in the hydration layer of a type III anti-freeze protein.
Z. F. Brotzakis, I. Voets, H. Bakker, P. Bolhuis
2018Physical Chemistry, Chemical Physics - PCCP20 citations Open access
Semantic Scholar
A maximum caliber approach for continuum path ensembles
P. Bolhuis, Z. F. Brotzakis, M. Vendruscolo
2021European Physical Journal B : Condensed Matter Physics19 citations Open access
Semantic Scholar
Exploration and Exploitation Approaches Based on Generative Machine Learning to Identify Potent Small Molecule Inhibitors of α-Synuclein Secondary Nucleation
Robert I. Horne, M. Murtada, D. Huo, Z. F. Brotzakis +4 more
2023Journal of Chemical Theory and Computation18 citations Open access
Semantic Scholar
Bayesian calibration of force-fields from experimental data: TIP4P water.
Ritabrata Dutta, Z. F. Brotzakis, A. Mira
2018Journal of Chemical Physics18 citations Open access
Semantic Scholar
Stability and growth mechanism of self-assembling putative antifreeze cyclic peptides.
Z. F. Brotzakis, Mascha Gehre, I. Voets, P. Bolhuis
2017Physical Chemistry, Chemical Physics - PCCP15 citations Open access
Semantic Scholar
Controversial Effects of D-Amino Acid Oxidase Activator (DAOA)/G72 on D-Amino Acid Oxidase (DAO) Activity in Human Neuronal, Astrocyte and Kidney Cell Lines: The N-methyl D-aspartate (NMDA) Receptor Hypofunction Point of View
V. Jagannath, Z. F. Brotzakis, M. Parrinello, S. Walitza +1 more
2017Frontiers in Molecular Neuroscience15 citations Open access
Semantic Scholar
Optimization of a small molecule inhibitor of secondary nucleation in α-synuclein aggregation
Roxine Staats, Z. F. Brotzakis, Sean Chia, Robert I. Horne +1 more
2023Frontiers in Molecular Biosciences13 citations Open access
Semantic Scholar
Transient interactions between the fuzzy coat and the cross-β core of brain-derived Aβ42 filaments
Maria Milanesi, Z. F. Brotzakis, M. Vendruscolo
2024bioRxiv11 citations Open access
Semantic Scholar
Design of Tau Aggregation Inhibitors Using Iterative Machine Learning and a Polymorph-Specific Brain-Seeded Fibril Amplification Assay
A. Santambrogio, Robert I. Horne, Michael A. Metrick, Nicholas C. T. Gallagher +8 more
2025bioRxiv10 citations Open access
Semantic Scholar
MD-LLM-1: A Large Language Model for Molecular Dynamics
M. Murtada, Z. F. Brotzakis, Michele Vendruscolo
20259 citations
Semantic Scholar
Using Generative Modeling to Endow with Potency Initially Inert Compounds with Good Bioavailability and Low Toxicity
Robert I. Horne, Jared Wilson-Godber, Alicia González Díaz, Z. F. Brotzakis +5 more
2024Journal of Chemical Information and Modeling9 citations Open access
Semantic Scholar
Discovery of the First-in-Class Inhibitors of Hypoxia Up-Regulated Protein 1 (HYOU1) Suppressing Pathogenic Fibroblast Activation.
D. Papadopoulou, Vasiliki Mavrikaki, F. Charalampous, C. Tzaferis +12 more
2024Angewandte Chemie9 citations Open access
Semantic Scholar
Unbiased Atomistic Insight into the Mechanisms and Solvent Role for Globular Protein Dimer Dissociation
Z. F. Brotzakis, P. Bolhuis
2018bioRxiv9 citations Open access
Semantic Scholar
Language Models for Molecular Dynamics
M. Murtada, Z. F. Brotzakis, M. Vendruscolo
2024bioRxiv6 citations Open access
Semantic Scholar
Identification of potent high-affinity secondary nucleation inhibitors of Aβ42 aggregation from an ultra-large chemical library using deep docking
Michaela Brezinova, Z. F. Brotzakis, Robert I. Horne, Vaidehi Roy Chowdhury +5 more
2025Molecular Systems Biology5 citations Open access
Semantic Scholar
Force field optimization by imposing kinetic constraints with path reweighting
P. Bolhuis, Z. F. Brotzakis, B. Keller
20225 citations
Semantic Scholar
Supplemental Materials : Augmented Harmonic Linear Discriminant Analysis
Z. F. Brotzakis, Dan Mendels, M. Parrinello
20193 citations
Semantic Scholar
Small Molecules Targeting the Structural Dynamics of AR-V7 Partially Disordered Proteins Using Deep Ensemble Docking
Pantelis Karatzas, Z. F. Brotzakis, H. Sarimveis
2025Journal of Chemical Theory and Computation2 citations Open access
Semantic Scholar
Design of Protein Sequences with Precisely Tuned Kinetic Properties
Z. F. Brotzakis, M. Vendruscolo, Georgios Skretas
2025bioRxiv2 citations Open access
Semantic Scholar
Destabilization of Helix III Initiates Early Serum Amyloid A Misfolding by Exposing Its Amyloidogenic Core
Haidara Nadwa, Z. F. Brotzakis, Annalisa Santucci, D. Braconi +1 more
2025bioRxiv2 citations Open access
Semantic Scholar
AlphaFold-Metainference: Prediction of Structural Ensembles of Disordered Proteins
Z. F. Brotzakis, Shengyu Zhang, M. Murtada, M. Vendruscolo
2024bioRxiv2 citations Open access
Semantic Scholar
A Machine Learning Approach to Identify Small Molecule Inhibitors of Secondary Nucleation in α-Synuclein Aggregation
Robert I. Horne, A. Possenti, Sean Chia, Z. F. Brotzakis +3 more
20222 citations Open access
Semantic Scholar
Guide for determination of protein structural ensembles by combining cryo‐EM data with metadynamics
Z. F. Brotzakis
2022FEBS Open Bio1 citations Open access
Semantic Scholar
A nested shell structure coordinates enzyme communication in pyruvate oxidation
Toni K. Träger, Sourav Maity, F. Kyrilis, Christian Tüting +9 more
2026bioRxiv0 citations Open access
Semantic Scholar
Anneal-MaxCal: kinetic ensembles from a Markov model learned along a solute-tempering ladder
Z. F. Brotzakis, N. Rekatsinas
2026bioRxiv0 citations Open access
Semantic Scholar
Correction to “Design of Tau Aggregation Inhibitors Using Iterative Machine Learning and a Polymorph-Specific Brain-Seeded Fibril Amplification Assay”
A. Santambrogio, Robert I. Horne, Michael A. Metrick, Nicholas C. T. Gallagher +8 more
2026Journal of the American Chemical Society0 citations Open access
Semantic Scholar
MD-LLM-2: A Transferable Language Model of Molecular Dynamics with Physical Conditioning and Explicit Path Probabilities
M. Murtada, Z. F. Brotzakis, Michele Vendruscolo
20260 citations
Semantic Scholar
Structure-based Generation of a Secondary Nucleation Inhibitor in α-Synuclein Aggregation Using a Conditional Diffusion Model
Hao Zhang, Robert I. Horne, Z. F. Brotzakis, Charles Harris +2 more
2025bioRxiv0 citations Open access
Semantic Scholar
Small molecules targeting the structural dynamics of AR-V7 partially disordered protein using deep learning and physics based models
P. Karatzas, Z. F. Brotzakis, H. Sarimveis
2024bioRxiv0 citations Open access
Semantic Scholar
Cryo-electron Microscopy and Molecular Modeling Methods to Characterize the Dynamics of Tau Bound to Microtubules.
Z. F. Brotzakis
2024Methods in molecular biology0 citations
Semantic Scholar
Where cryo-electron and computational microscopy converge: The story of the elusive flipback conformation of protein kinase A and its critical role in phosphodiesterase cyclic AMP channeling
Sophia P. Hirakis, Varun Venkatakrishnan, Z. F. Brotzakis, Jian Wu +3 more
2024Biophysical Journal0 citations
Semantic Scholar

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