Li-Yen Yang, Kaike Ping, Yunan Luo, Andrew C. McShan
{"title":"BioDolphin as a comprehensive database of lipid–protein binding interactions","authors":"Li-Yen Yang, Kaike Ping, Yunan Luo, Andrew C. McShan","doi":"10.1038/s42004-024-01384-z","DOIUrl":null,"url":null,"abstract":"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. Lipid–protein interactions are crucial for virtually all biological processes in living cells, however, systematic structural databases covering broad types of lipid–protein interaction are lacking. Here, the authors develop BioDolphin, a curated database with over 127,000 lipid–protein interactions, providing comprehensive annotations detailing lipid–protein complexes.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":" ","pages":"1-11"},"PeriodicalIF":5.9000,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01384-z.pdf","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Communications Chemistry","FirstCategoryId":"92","ListUrlMain":"https://www.nature.com/articles/s42004-024-01384-z","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
引用次数: 0
Abstract
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. Lipid–protein interactions are crucial for virtually all biological processes in living cells, however, systematic structural databases covering broad types of lipid–protein interaction are lacking. Here, the authors develop BioDolphin, a curated database with over 127,000 lipid–protein interactions, providing comprehensive annotations detailing lipid–protein complexes.
期刊介绍:
Communications Chemistry is an open access journal from Nature Research publishing high-quality research, reviews and commentary in all areas of the chemical sciences. Research papers published by the journal represent significant advances bringing new chemical insight to a specialized area of research. We also aim to provide a community forum for issues of importance to all chemists, regardless of sub-discipline.