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It was a great pleasure to introduce our inverse folding molecular dynamics work to design nanobodies for unbinding kinetics from predetermined targets during the "Designing Kinetics: from Modeling to Optimization and back again" Lorentz Center workshop in Leiden 13-17 October 2025, in front of a great audience of experts in the field! Acknowledgements to @boost4bio for funding and the organizers for participation.
Happy to have contributed to this paper entitled "Design of Tau Aggregation Inhibitors Using Iterative Machine Learning and a Polymorph-Specific Brain-Seeded Fibril Amplification Assay" together with Vendruscolo lab that just came out in JACS
It was a great pleasure to introduce our inverse folding molecular dynamics work to design nanobodies for unbinding kinetics from predetermined targets during the "69th Protein structure prediction and design in biology and pharmacology" symposium#benzon25 in Copenhagen in front of a great audience of experts in the field! Acknowledgements to @boost4bio for funding and the organizers for participation.
Very happy to share our new work Small Molecules Targeting the Structural Dynamics of AR-V7 Partially Disordered Proteins Using Deep Ensemble Docking" has been published in JCTC. This work enable structure based in silico screening for small molecule binders against disordered protein ensembles. It presents a pipeline to generate structural ensembles, identify a handful of meaningful binding sites, ensemble dock small molecules and train an ML model to explore the large chemical space for binders at these sites. This works has been a collaboration between BSRC Fleming, U. Cambridge and NTUA.
Happy to give an invited talk entitled 'Data driven physics and machine learning based approaches for determining atomistic protein dynamics and potent inhibitors of pathological targets involved in disease' on Monday 24-2-25, @14.30 EET in Athena Research Center at the Archimedes - AI and Data Science Research Hub
Possible to attend online as well (see link)
Very happy to share our new work "Design of Protein Sequences with Precisely Tuned Kinetic Properties" together with Michele Vendruscolo and Georgios Skretas, a collaboration between BSRC Alexander Fleming and University of Cambridge. https://lnkd.in/dfVHZMUn
We strive to design protein sequences with tailored protein dynamics and consequent macroscopic properties by using free energy landscapes from#MD and #InverseFolding, pioneered by Pratyush Tiwary & Michele Parrinello and Justas Dauparas, PhD & David Baker @Institute for Protein Design, University of Washington
2025. New paper in Nature Communications. 🎉
Brotzakis, Z.F., Zhang, S., Murtada, M.H. et al. AlphaFold prediction of structural ensembles of disordered proteins. Nat Commun 16, 1632 (2025).
Interview about our method in Greek, from Vasiliki Michopoulou @Dnews.gr
2025. New paper in science advances!!🎉
Transient interactions between the fuzzy coat and the cross-β core of brain-derived Aβ42 filaments.Sci. Adv.11,eadr7008(2025).DOI:10.1126/sciadv.adr7008
Interview about our work from Maria Kouzinopoulou @Amna.gr
5th International Conference on Materials Science & Nanotechnology (Future Materials-2024), invited speaker
2024, Invited talk on "Computational Design of Antibodies Against Disease-Related Molecular Targets" @ 7th Conference of Young Scientists Hellenic Pasteur Institute.
2024, new paper in Nature Chemical biology: "Discovery of potent inhibitors of α-synuclein aggregation using structure-based iterative learning. Nat Chem Biol (2024)" link
2024, new book chapter contribution in Springer: "Cryo-electron Microscopy and Molecular Modeling Methods to Characterize the Dynamics of Tau Bound to Microtubules. Methods in Molecular Biology, 77–90 (2024)" link
2024, new article:"Discovery of the First‐in‐Class Inhibitors of Hypoxia Up‐Regulated Protein 1 (HYOU1) Suppressing Pathogenic Fibroblast Activation" Angew Chem Int Ed (2024) link
2024, new article:"Using Generative Modeling to Endow with Potency Initially Inert Compounds with Good Bioavailability & Low Toxicity" in JCIM link
2023, Academy of Athens Award on "Pioneering Research Article in the Field of Chemistry, G. Fotinos". Here is a recent interview (in Greek) to APE-MPE
(2023)New research is out: "Multiplexed Digital Characterization of Misfolded Protein Oligomers via Solid-State Nanopores" in JACS link
(2023)Our new article: "Optimizing molecular potential models by imposing kinetic constraints with path reweighting" with Peter Bolhuis and Bettna Keller, made it to JCP special edition "Machine Learning Hits Molecular Simulations" as well as to the cover! link
(2023)#Biochemistry publication#. Z. F. Brotzakis, T. Löhr, S. Truong, S. Hoff, M. Bonomi, & M. Vendruscolo. Determination of the Structure and Dynamics of the Fuzzy Coat of an Amyloid Fibril of IAPP Using Cryo-Electron Microscopy Biochemistry Article ASAP DOI: 10.1021/acs.biochem.3c00010 link
(2023)New JCTC publication: R. I. Horne, M. H. Murtada, Donghui Huo, Z. F. Brotzakis, R. C. Gregory, A. Possenti, S. Chia, and M. Vendruscolo. Exploration and Exploitation Approaches Based on Generative Machine Learning to Identify Potent Small Molecule Inhibitors of α-Synuclein Secondary Nucleation JCTC Article ASAP 2023 link
(2023)New Nature comm. article: 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
(2023)New preprint Brotzakis Z. F., Zhang S & Vendruscolo M. (2023) AlphaFold Prediction of Structural Ensembles of Disordered Proteins doi: 10.1101/2023.01.19.524720
(2023)New article for facile use of MEMMI: Brotzakis Z. F*. (2023) Guide for determination of protein structural ensembles by combining Cryo-EM data with metadynamics. FEBS Open Bio https://doi.org/10.1002/2211-5463.1354
(2022) Interview of FEBS long-term fellows having participated in the FEBS Fellows Meeting 2022 (Vimeiro, Portugal) featuring in FEBS news
(2022)Invited speaker at the annual Hellenic Society of Biochemistry and Molecular Biology (Patras, GR)
(2022) Invited speaker at the "20 years of Metadynamics" CECAM meeting (Lausanne, CH)
Sept 2022: Awarded a 2 year post-doctoral fellowship from the Bodossakis foundation, between University of Cambridge (M. Vendruscolo) and BSRC Fleming (G. Skretas)
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