The MemProtMD database: A resource for membrane-embedded protein structures and their lipid interactions
Integral membrane proteins fulfil important roles in many crucial biological processes, including cell signalling, molecular transport and bioenergetic processes. Advancements in experimental techniques are revealing high resolution structures for an increasing number of membrane proteins. Yet, thes...
| Main Authors: | , , |
|---|---|
| Format: | Journal article |
| Published: |
Oxford University Press
2018
|
| _version_ | 1797099604099989504 |
|---|---|
| author | Newport, T Sansom, M Stansfeld, P |
| author_facet | Newport, T Sansom, M Stansfeld, P |
| author_sort | Newport, T |
| collection | OXFORD |
| description | Integral membrane proteins fulfil important roles in many crucial biological processes, including cell signalling, molecular transport and bioenergetic processes. Advancements in experimental techniques are revealing high resolution structures for an increasing number of membrane proteins. Yet, these structures are rarely resolved in complex with membrane lipids. In 2015, the MemProtMD pipeline was developed to allow the automated lipid bilayer assembly around new membrane protein structures, released from the Protein Data Bank. To make this data available to the scientific community, a web database (http://memprotmd.bioch.ox.ac.uk) has been developed. Simulations and the results of subsequent analysis can be viewed using a web browser, including interactive 3D visualisations of the assembled bilayer and 2D visualisations of lipid contact data and membrane protein topology. In addition, ensemble analyses are performed to detail conserved lipid interaction information across proteins, families and for the entire database of 3506 PDB entries. Proteins may be searched using keywords, PDB or Uniprot identifier, or browsed using classification systems such as Pfam, Gene Ontology annotation, mpstruc or the Transporter Classification Database. All files required to run further molecular simulations of proteins in the database are provided. |
| first_indexed | 2024-03-07T05:26:01Z |
| format | Journal article |
| id | oxford-uuid:e095225b-67e0-4124-b652-96a637a98796 |
| institution | University of Oxford |
| last_indexed | 2024-03-07T05:26:01Z |
| publishDate | 2018 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | oxford-uuid:e095225b-67e0-4124-b652-96a637a987962022-03-27T09:48:19ZThe MemProtMD database: A resource for membrane-embedded protein structures and their lipid interactionsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:e095225b-67e0-4124-b652-96a637a98796Symplectic Elements at OxfordOxford University Press2018Newport, TSansom, MStansfeld, PIntegral membrane proteins fulfil important roles in many crucial biological processes, including cell signalling, molecular transport and bioenergetic processes. Advancements in experimental techniques are revealing high resolution structures for an increasing number of membrane proteins. Yet, these structures are rarely resolved in complex with membrane lipids. In 2015, the MemProtMD pipeline was developed to allow the automated lipid bilayer assembly around new membrane protein structures, released from the Protein Data Bank. To make this data available to the scientific community, a web database (http://memprotmd.bioch.ox.ac.uk) has been developed. Simulations and the results of subsequent analysis can be viewed using a web browser, including interactive 3D visualisations of the assembled bilayer and 2D visualisations of lipid contact data and membrane protein topology. In addition, ensemble analyses are performed to detail conserved lipid interaction information across proteins, families and for the entire database of 3506 PDB entries. Proteins may be searched using keywords, PDB or Uniprot identifier, or browsed using classification systems such as Pfam, Gene Ontology annotation, mpstruc or the Transporter Classification Database. All files required to run further molecular simulations of proteins in the database are provided. |
| spellingShingle | Newport, T Sansom, M Stansfeld, P The MemProtMD database: A resource for membrane-embedded protein structures and their lipid interactions |
| title | The MemProtMD database: A resource for membrane-embedded protein structures and their lipid interactions |
| title_full | The MemProtMD database: A resource for membrane-embedded protein structures and their lipid interactions |
| title_fullStr | The MemProtMD database: A resource for membrane-embedded protein structures and their lipid interactions |
| title_full_unstemmed | The MemProtMD database: A resource for membrane-embedded protein structures and their lipid interactions |
| title_short | The MemProtMD database: A resource for membrane-embedded protein structures and their lipid interactions |
| title_sort | memprotmd database a resource for membrane embedded protein structures and their lipid interactions |
| work_keys_str_mv | AT newportt thememprotmddatabasearesourceformembraneembeddedproteinstructuresandtheirlipidinteractions AT sansomm thememprotmddatabasearesourceformembraneembeddedproteinstructuresandtheirlipidinteractions AT stansfeldp thememprotmddatabasearesourceformembraneembeddedproteinstructuresandtheirlipidinteractions AT newportt memprotmddatabasearesourceformembraneembeddedproteinstructuresandtheirlipidinteractions AT sansomm memprotmddatabasearesourceformembraneembeddedproteinstructuresandtheirlipidinteractions AT stansfeldp memprotmddatabasearesourceformembraneembeddedproteinstructuresandtheirlipidinteractions |