Yang Li-Yen, Ping Kaike, Luo Yunan, McShan Andrew C
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA.
Commun Chem. 2024 Dec 4;7(1):288. doi: 10.1038/s42004-024-01384-z.
Lipid-protein interactions are crucial for virtually all biological processes in living cells. However, existing structural databases focusing on these interactions are limited to integral membrane proteins. A systematic understanding of diverse lipid-protein interactions also encompassing lipid-anchored, peripheral membrane and soluble lipid binding proteins remains to be elucidated. To address this gap and facilitate the research of universal lipid-protein assemblies, we developed BioDolphin - a curated database with over 127,000 lipid-protein interactions. BioDolphin provides comprehensive annotations, including protein functions, protein families, lipid classifications, lipid-protein binding affinities, membrane association type, and atomic structures. Accessible via a publicly available web server ( www.biodolphin.chemistry.gatech.edu ), users can efficiently search for lipid-protein interactions using a wide range of options and download datasets of interest. Additionally, BioDolphin features interactive 3D visualization of each lipid-protein complex, facilitating the exploration of structure-function relationships. BioDolphin also includes detailed information on atomic-level intermolecular interactions between lipids and proteins that enable large scale analysis of both paired complexes and larger assemblies. As an open-source resource, BioDolphin enables global analysis of lipid-protein interactions and supports data-driven approaches for developing predictive machine learning algorithms for lipid-protein binding affinity and structures.
脂类-蛋白质相互作用对活细胞中几乎所有的生物过程都至关重要。然而，现有的专注于这些相互作用的结构数据库仅限于整合膜蛋白。对包括脂锚定、外周膜和可溶性脂结合蛋白在内的各种脂类-蛋白质相互作用的系统理解仍有待阐明。为了填补这一空白并促进对通用脂类-蛋白质组装体的研究，我们开发了BioDolphin——一个拥有超过12.7万个脂类-蛋白质相互作用的精选数据库。BioDolphin提供了全面的注释，包括蛋白质功能、蛋白质家族、脂类分类、脂类-蛋白质结合亲和力、膜关联类型和原子结构。通过公开可用的网络服务器（www.biodolphin.chemistry.gatech.edu），用户可以使用多种选项高效搜索脂类-蛋白质相互作用，并下载感兴趣的数据集。此外，BioDolphin具有每个脂类-蛋白质复合物的交互式3D可视化功能，便于探索结构-功能关系。BioDolphin还包括关于脂类和蛋白质之间原子水平分子间相互作用的详细信息，能够对成对复合物和更大的组装体进行大规模分析。作为一个开源资源，BioDolphin能够对脂类-蛋白质相互作用进行全球分析，并支持数据驱动的方法来开发用于预测脂类-蛋白质结合亲和力和结构的机器学习算法。
