EM Data Bank
 | |
|---|---|
| Content | |
| Description | Unified Data Resource for CryoEM. |
| Contact | |
| Research center | European Bioinformatics Institute (UK site) AND Rutgers University (USA site) |
| Laboratory | PDBe & RCSB PDB |
| Primary citation | Lawson & al. (2011)[1] |
| Release date | 2002 |
| Access | |
| Website | http://emdatabank.org |
| Tools | |
| Miscellaneous | |
The EM Data Bank or Electron Microscopy Data Bank (EMDB) collects 3D EM maps and associated experimental data determined using electron microscopy of biological specimens. It was established in 2002 at the MSD/PDBe group of the European Bioinformatics Institute (EBI), where the European site of the EMDataBank.org consortium is located. As of 2015, the resource contained over 2,600 entries with a mean resolution of 15Å.[2]
It provides both the
Under the NIH Unified Data Resource for CryoEM, the Research Collaboration for Structural Biology (RCSB) also acts as a deposition, data processing and distribution center for EMDB data, while the National Center for Macromolecular Imaging (NCMI) is a collaborative partner in providing services and tools concerning the EMDB.
EMDB is an archive for three-dimensional density maps of all types of biological assemblies, including ribosomes, chaperones, polymerases, multifunctional enzymes and viruses. Viper EMDB at Scripps is a separate database for three-dimensional EM maps of viruses.
See also
References
- ↑ Lawson, Catherine L; Baker Matthew L, Best Christoph, Bi Chunxiao, Dougherty Matthew, Feng Powei, van Ginkel Glen, Devkota Batsal, Lagerstedt Ingvar, Ludtke Steven J, Newman Richard H, Oldfield Tom J, Rees Ian, Sahni Gaurav, Sala Raul, Velankar Sameer, Warren Joe, Westbrook John D, Henrick Kim, Kleywegt Gerard J, Berman Helen M, Chiu Wah (Jan 2011). "EMDataBank.org: unified data resource for CryoEM". Nucleic Acids Res. (England) 39 (Database issue): D456–64. doi:10.1093/nar/gkq880. PMC 3013769. PMID 20935055. Cite uses deprecated parameter
|coauthors=(help) - ↑ Esquivel-Rodríguez J, Xiong Y, Han X, Guang S, Christoffer C, Kihara D (30 May 2015). "Navigating 3D electron microscopy maps with EM-SURFER". BMC Bioinform. 16 (181). doi:10.1186/s12859-015-0580-6. PMID 26025554.
- Tagari, M.; et al. (2002). "New electron microscopy database and deposition system". Trends Biochem Sci 27 (11): 589. doi:10.1016/s0968-0004(02)02176-x. PMID 12417136.
- Fuller, S. D. (2003). "Depositing electron microscopy maps". Structure 11 (1): 11–12. doi:10.1016/s0969-2126(02)00942-5. PMID 12517335.
- "EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information". J. Struct. Biol. 144 (1-2): 228–37. 2003. doi:10.1016/j.jsb.2003.09.009. PMID 14643225.
- Heymann, J. B.; Chagoyen, M.; Belnap, D. M. (2005). "Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology". J Struct Biol 151 (2): 196–207. doi:10.1016/j.jsb.2005.06.001. PMID 16043364.
- Tagari, M.; et al. (2006). "E-MSD: improving data deposition and structure quality". Nucleic Acids Res 34 (90001): 287–290. doi:10.1093/nar/gkj163. PMC 1347525. PMID 16381867.
- "EMDataBank.org: unified data resource for CryoEM". Nucleic Acids Res. 39 (Database issue): D456–64. January 2011. doi:10.1093/nar/gkq880. PMC 3013769. PMID 20935055.
External links
- Software tools for molecular microscopy
- EM Data Bank
- US and UK Search pages
- Japan Search page (EM Navigator in PDBj)