The rapid evolution of computational structural biology, driven by AI, continues to revolutionise our understanding of biomolecular structures, functions, and interactions. This follow-up to the 2023 first edition of the workshop responds to the field’s swift advancements and the pressing need for a forum that not only aligns with these progresses but also foresees future shifts. The conference aims to advance computational structural biology, promote the adoption of innovative methodologies, and enhance interdisciplinary research and collaborations. Capturing the latest advancements in this vibrant field, this second edition of the meeting is set to provide a pivotal platform for disseminating these breakthroughs and charting future directions in computational structural biology.