Abstract
The introduction of AlphaFold2 1, its subsequent AlphaFold3 version 2, and the public release of hundreds of millions of protein structures predicted by this landmark method 3,4 have fundamentally changed the fields of structural biology and protein bioinformatics.Structural biology, which once relied on painstaking and relatively slow experimental determination of protein structure, has become one of abundance, with structural models now available for nearly every known protein sequence.Protein bioinformatics has evolved from developing structure prediction tools to analyzing and applying structural models.This special issue of the Computational and Structural Biotechnology Journal commemorates these transitions by exploring the many diverse ways in which AlphaFold is used.We initiated this special issue in July of 2024 and were flooded with submissions.We extended the original submission deadline from October 31, 2024, to January 31, 2025, to accommodate this strong interest.The resulting special issue includes 32 articles that collectively define the current state of structural protein bioinformatics.We are deeply grateful to the authors who entrusted us with their studies, the reviewers who provided their timely and insightful advice, and the editorial team for their help with this process and encouragement to organize this special issue.Following, we provide a brief overview of our special issue.