E-MSD: the European Bioinformatics Institute Macromolecular Structure Database - PubMed (original) (raw)
. 2003 Jan 1;31(1):458-62.
doi: 10.1093/nar/gkg065.
D Dimitropoulos, J Fillon, A Golovin, K Henrick, A Hussain, J Ionides, M John, P A Keller, E Krissinel, P McNeil, A Naim, R Newman, T Oldfield, J Pineda, A Rachedi, J Copeland, A Sitnov, S Sobhany, A Suarez-Uruena, J Swaminathan, M Tagari, J Tate, S Tromm, S Velankar, W Vranken
Affiliations
- PMID: 12520052
- PMCID: PMC165512
- DOI: 10.1093/nar/gkg065
E-MSD: the European Bioinformatics Institute Macromolecular Structure Database
H Boutselakis et al. Nucleic Acids Res. 2003.
Abstract
The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool.
Figures
Figure 1
The E-MSD database core entity relationships. Each level of the hierarchy can have associated properties, e.g. Bound molecules, Domains definitions, Site residues, Derived properties (e.g. Accessible Surface Area), Reference information (e.g. standard geometry).
Figure 2
Sample SMILES based search using chempdb and starting from 3-chorophenol, (a) selected search results using the ‘has substructure’ option wherein the results have the connected fragment, and (b) selected search results using the fingerprint option where the matching ligands contain the chemical constituents of the query structure. The matched compounds shown are: TCL 5-chloro-2-(2,4-dichlorophenoxy)phenol, EAA [2,3-dichloro-4-(2-ethylacryloyl)phenoxy]acetic acid, CHB 3-chloro-4-hydroxybenzoic acid, and CFA 2,4-dichlorophenoxy acetic acid.
Figure 3
The process is driven by a number of dictionaries describing the database-model (Database Definition), interface contents and layout (Search page definition, Result page definition) or the description useful in construction of the SQL query (Search tools, Result tools). The system uses the XML-XSL technology to generate HTML pages using AxKit module.
Similar articles
- E-MSD: an integrated data resource for bioinformatics.
Velankar S, McNeil P, Mittard-Runte V, Suarez A, Barrell D, Apweiler R, Henrick K. Velankar S, et al. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D262-5. doi: 10.1093/nar/gki058. Nucleic Acids Res. 2005. PMID: 15608192 Free PMC article. - E-MSD: an integrated data resource for bioinformatics.
Golovin A, Oldfield TJ, Tate JG, Velankar S, Barton GJ, Boutselakis H, Dimitropoulos D, Fillon J, Hussain A, Ionides JM, John M, Keller PA, Krissinel E, McNeil P, Naim A, Newman R, Pajon A, Pineda J, Rachedi A, Copeland J, Sitnov A, Sobhany S, Suarez-Uruena A, Swaminathan GJ, Tagari M, Tromm S, Vranken W, Henrick K. Golovin A, et al. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D211-6. doi: 10.1093/nar/gkh078. Nucleic Acids Res. 2004. PMID: 14681397 Free PMC article. - E-MSD: improving data deposition and structure quality.
Tagari M, Tate J, Swaminathan GJ, Newman R, Naim A, Vranken W, Kapopoulou A, Hussain A, Fillon J, Henrick K, Velankar S. Tagari M, et al. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D287-90. doi: 10.1093/nar/gkj163. Nucleic Acids Res. 2006. PMID: 16381867 Free PMC article. - The Protein Data Bank Archive.
Velankar S, Burley SK, Kurisu G, Hoch JC, Markley JL. Velankar S, et al. Methods Mol Biol. 2021;2305:3-21. doi: 10.1007/978-1-0716-1406-8_1. Methods Mol Biol. 2021. PMID: 33950382 Review. - EMBL's European Bioinformatics Institute (EMBL-EBI) in 2023.
Thakur M, Buniello A, Brooksbank C, Gurwitz KT, Hall M, Hartley M, Hulcoop DG, Leach AR, Marques D, Martin M, Mithani A, McDonagh EM, Mutasa-Gottgens E, Ochoa D, Perez-Riverol Y, Stephenson J, Varadi M, Velankar S, Vizcaino JA, Witham R, McEntyre J. Thakur M, et al. Nucleic Acids Res. 2024 Jan 5;52(D1):D10-D17. doi: 10.1093/nar/gkad1088. Nucleic Acids Res. 2024. PMID: 38015445 Free PMC article. Review.
Cited by
- Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology.
Behzadi P, Gajdács M. Behzadi P, et al. Eur J Microbiol Immunol (Bp). 2021 Dec 15;11(4):77-86. doi: 10.1556/1886.2021.00020. Print 2022 Feb 3. Eur J Microbiol Immunol (Bp). 2021. PMID: 34908533 Free PMC article. Review. - Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction.
Burley SK, Berman HM. Burley SK, et al. Structure. 2021 Jun 3;29(6):515-520. doi: 10.1016/j.str.2021.04.010. Epub 2021 May 12. Structure. 2021. PMID: 33984281 Free PMC article. Review. - Swiss-PO: a new tool to analyze the impact of mutations on protein three-dimensional structures for precision oncology.
Krebs FS, Zoete V, Trottet M, Pouchon T, Bovigny C, Michielin O. Krebs FS, et al. NPJ Precis Oncol. 2021 Mar 18;5(1):19. doi: 10.1038/s41698-021-00156-5. NPJ Precis Oncol. 2021. PMID: 33737716 Free PMC article. - The data universe of structural biology.
Berman HM, Vallat B, Lawson CL. Berman HM, et al. IUCrJ. 2020 May 28;7(Pt 4):630-638. doi: 10.1107/S205225252000562X. eCollection 2020 Jul 1. IUCrJ. 2020. PMID: 32695409 Free PMC article. Review. - APOBEC3H structure reveals an unusual mechanism of interaction with duplex RNA.
Bohn JA, Thummar K, York A, Raymond A, Brown WC, Bieniasz PD, Hatziioannou T, Smith JL. Bohn JA, et al. Nat Commun. 2017 Oct 18;8(1):1021. doi: 10.1038/s41467-017-01309-6. Nat Commun. 2017. PMID: 29044109 Free PMC article.
References
- Service R.F. (2000) Structural genomics offers high-speed look at proteins. Science, 287, 194–196. - PubMed
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources