Abstract
The protein universe remains only partially explored, with many protein families and functions yet to be discovered. Leveraging large-scale protein sequence and structure datasets, we recently developed an unsupervised representation of this landscape that reveals functionally relevant clusters across millions of proteins. This data-driven approach enables the prioritization and characterization of unknown protein families, providing candidates for experimental validation. Using this framework, we uncovered novel biology at an unprecedented scale, including previously unknown prokaryotic defense systems and a new protein fold. This work underscores the power of AI-guided discovery and lays the foundation for a dynamic, continually evolving atlas of the protein universe, accelerating our understanding of molecular function and evolution across life.
Short bio
Joana Pereira leads the “Protein Evolution and Function Models” group at the newly established VIB Center for AI and Computational Biology in Leuven and is an Assistant Professor at the Department of Cellular and Molecular Medicine at KU Leuven since February 2025. She is an expert in computational structural biology and protein evolution, with a strong background in structural bioinformatics. Joana holds a doctorate in Chemistry from the University of Hamburg and the European Molecular Biology Laboratory, and is trained as a biochemist. She has over seven years of postdoctoral experience in protein evolution and structural bioinformatics, having worked at the Max Planck Institute for Developmental Biology in Tübingen and the Biozentrum at the University of Basel. Her research applies computer science, complex network analysis, and deep learning to explore the structure, diversity, and evolution of the protein universe. Although fundamentally computational, her work is highly interdisciplinary and includes close collaborations with experimentalists, particularly in the study of prokaryotic interactions with the environment.