Abstract: The transformative breakthroughs of the AlphaFold series in structural biology are often attributed to algorithmic advances, yet the critical role of its evolving data strategy remains underexplored. Adopting a data-centric perspective, this paper deconstructs the iterative mechanisms driving AlphaFold’s progress from versions 1 to 3, emphasizing the optimization of data quality attributes, innovations in representation paradigms, and data-model synergy. The analysis reveals that each performance leap stems from the co-evolution of data and model architectures. AlphaFold’s data strategy follows a clear trajectory: from passive data adoption, to proactive data construction, and finally to generative data augmentation. From this, three core principles emerge: paradigm shifts in data representation are the primary drivers of breakthroughs; data-model co-evolution is a hallmark of system maturity; and the richness of data quality attributes sets the ceiling for an AI’s learning potential. These principles yield four implications for the AI for Science (AI4S) field: data practices should shift from passive preparation to active design; research should prioritize data-model alignment over model- or data-centric approaches; data ecosystems should focus on enhancing key attributes, such as diversity and quality, rather than broad multimodal integration; and a new theoretical and evaluation framework is needed to assess the "scientific efficacy" of data. This study provides a theoretical foundation and practical roadmap for advancing AI-driven scientific discovery.

Key words: AlphaFold')">

AlphaFold, scientific data, data-model synergy, protein structure prediction, AI for science