Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India.
Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
Database (Oxford). 2024 Sep 19;2024. doi: 10.1093/database/baae088.
Autophagy pathway plays a central role in cellular degradation. The proteins involved in the core autophagy process are mostly localised on membranes or interact indirectly with lipid-associated proteins. Therefore, progress in structure determination of 'core autophagy proteins' remained relatively limited. Recent paradigm shift in structural biology that includes cutting-edge cryo-EM technology and robust AI-based Alphafold2 predicted models has significantly increased data points in biology. Here, we developed Autophagy3D, a web-based resource that provides an efficient way to access data associated with 40 core human autophagic proteins (80322 structures), their protein-protein interactors and ortholog structures from various species. Autophagy3D also offers detailed visualizations of protein structures, and, hence deriving direct biological insights. The database significantly enhances access to information as full datasets are available for download. The Autophagy3D can be publicly accessed via https://autophagy3d.igib.res.in. Database URL: https://autophagy3d.igib.res.in.
自噬途径在细胞降解中起着核心作用。参与核心自噬过程的蛋白质大多位于膜上或与脂相关蛋白间接相互作用。因此，“核心自噬蛋白”的结构测定进展相对有限。结构生物学的最新范式转变，包括最先进的冷冻电镜技术和基于强大人工智能的 Alphafold2 预测模型，大大增加了生物学中的数据点。在这里，我们开发了 Autophagy3D，这是一个基于网络的资源，提供了一种有效的方法来访问与 40 个人类核心自噬蛋白（80322 个结构）相关的数据，以及来自不同物种的其蛋白质-蛋白质相互作用者和同源结构。Autophagy3D 还提供了蛋白质结构的详细可视化，从而得出直接的生物学见解。该数据库大大增强了信息访问，因为可下载完整的数据集。Autophagy3D 可通过 https://autophagy3d.igib.res.in 公开访问。数据库网址：https://autophagy3d.igib.res.in。
