BioDolphin as a comprehensive database of lipid–protein binding interactions
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...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-12-01
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| Series: | Communications Chemistry |
| Online Access: | https://doi.org/10.1038/s42004-024-01384-z |
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| _version_ | 1846137279701057536 |
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| author | Li-Yen Yang Kaike Ping Yunan Luo Andrew C. McShan |
| author_facet | Li-Yen Yang Kaike Ping Yunan Luo Andrew C. McShan |
| author_sort | Li-Yen Yang |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-6e72d318fa1b41d5a9e2df6e19c5bd5c |
| institution | Kabale University |
| issn | 2399-3669 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Chemistry |
| spelling | doaj-art-6e72d318fa1b41d5a9e2df6e19c5bd5c2024-12-08T12:21:28ZengNature PortfolioCommunications Chemistry2399-36692024-12-017111110.1038/s42004-024-01384-zBioDolphin as a comprehensive database of lipid–protein binding interactionsLi-Yen Yang0Kaike Ping1Yunan Luo2Andrew C. McShan3School of Chemistry and Biochemistry, Georgia Institute of TechnologyDepartment of Computer Science, Virginia TechSchool of Computational Science and Engineering, Georgia Institute of TechnologySchool of Chemistry and Biochemistry, Georgia Institute of TechnologyAbstract 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.https://doi.org/10.1038/s42004-024-01384-z |
| spellingShingle | Li-Yen Yang Kaike Ping Yunan Luo Andrew C. McShan BioDolphin as a comprehensive database of lipid–protein binding interactions Communications Chemistry |
| title | BioDolphin as a comprehensive database of lipid–protein binding interactions |
| title_full | BioDolphin as a comprehensive database of lipid–protein binding interactions |
| title_fullStr | BioDolphin as a comprehensive database of lipid–protein binding interactions |
| title_full_unstemmed | BioDolphin as a comprehensive database of lipid–protein binding interactions |
| title_short | BioDolphin as a comprehensive database of lipid–protein binding interactions |
| title_sort | biodolphin as a comprehensive database of lipid protein binding interactions |
| url | https://doi.org/10.1038/s42004-024-01384-z |
| work_keys_str_mv | AT liyenyang biodolphinasacomprehensivedatabaseoflipidproteinbindinginteractions AT kaikeping biodolphinasacomprehensivedatabaseoflipidproteinbindinginteractions AT yunanluo biodolphinasacomprehensivedatabaseoflipidproteinbindinginteractions AT andrewcmcshan biodolphinasacomprehensivedatabaseoflipidproteinbindinginteractions |