E-MSD: improving data deposition and structure quality
- 1 January 2006
- journal article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 34 (90001) , D287-D290
- https://doi.org/10.1093/nar/gkj163
Abstract
The Macromolecular Structure Database (MSD) (http://www.ebi.ac.uk/msd/) [H. Boutselakis, D. Dimitropoulos, J. Fillon, A. Golovin, K. Henrick, A. Hussain, J. Ionides, M. John, P. A. Keller, E. Krissinel et al. (2003) E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Res., 31, 458-462.] group is one of the three partners in the worldwide Protein DataBank (wwPDB), the consortium entrusted with the collation, maintenance and distribution of the global repository of macromolecular structure data [H. Berman, K. Henrick and H. Nakamura (2003) Announcing the worldwide Protein Data Bank. Nature Struct. Biol., 10, 980.]. Since its inception, the MSD group has worked with partners around the world to improve the quality of PDB data, through a clean up programme that addresses inconsistencies and inaccuracies in the legacy archive. The improvements in data quality in the legacy archive have been achieved largely through the creation of a unified data archive, in the form of a relational database that stores all of the data in the wwPDB. The three partners are working towards improving the tools and methods for the deposition of new data by the community at large. The implementation of the MSD database, together with the parallel development of improved tools and methodologies for data harvesting, validation and archival, has lead to significant improvements in the quality of data that enters the archive. Through this and related projects in the NMR and EM realms the MSD continues to improve the quality of publicly available structural data.Keywords
This publication has 21 references indexed in Scilit:
- HalX: an open-source LIMS (Laboratory Information Management System) for small- to large-scale laboratoriesActa Crystallographica Section D-Biological Crystallography, 2005
- E-MSD: an integrated data resource for bioinformaticsNucleic Acids Research, 2004
- Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensionsActa Crystallographica Section D-Biological Crystallography, 2004
- The Uppsala Electron-Density ServerActa Crystallographica Section D-Biological Crystallography, 2004
- Design of a data model for developing laboratory information management and analysis systems for protein productionProteins-Structure Function and Bioinformatics, 2004
- MOLE: A data management application based on a protein production data modelProteins-Structure Function and Bioinformatics, 2004
- The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene OntologyNucleic Acids Research, 2004
- The InterPro Database, 2003 brings increased coverage and new featuresNucleic Acids Research, 2003
- SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic modelActa Crystallographica Section D-Biological Crystallography, 1999
- PQS: a protein quaternary structure file serverTrends in Biochemical Sciences, 1998