Nucleic Acids Research, 2006, Vol. 34, Database issue D287–D290 doi:10.1093/nar/gkj163 E-MSD: improving data deposition and structure quality M. Tagari, J. Tate, G. J. Swaminathan, R. Newman, A. Naim, W. Vranken, A. Kapopoulou, A. Hussain, J. Fillon, K. Henrick and S. Velankar* Macromolecular Structure Database, EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Received September 15, 2005; Revised and Accepted November 1, 2005 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 inconsisten- cies 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 con- tinues to improve the quality of publicly available structural data. INTRODUCTION Streamlining of protein cloning, expression, puriﬁcation through to crystallization and structure determination has res- ulted in rapid increase in the rate at which new structures are determined. It is becoming ever more important that the asso- ciated deposition tools keep pace with this exponential growth of data. The process of structure deposition is being adapted to cope with these rapid changes and remains an important step in the structure determination and publication pipeline. We are addressing the real problems that are involved with quickly and accurately annotating and archiving new structures to avoid the risk of disillusionment and disaffection amongst the structural biologists whose work populates data resources such as the Macromolecular Structure Database (MSD). To ensure that the core data is represented uniformly at all the worldwide Protein DataBank (wwPDB) partner sites, the three sites have active collaboration involving exchange of the core reference information (e.g. the dictionary description for lig- ands) and regular discussions to apply uniform standards for deposition and annotation of the core data. The MSD is approaching these problems in several ways. As a partner in the CCP4 project (1) we have contributed to the deﬁnition of standards for data harvesting and are working with CCP4 software developers to integrate the MSD depos- ition tool AutoDep into the CCP4 structure determination ﬂow. The CCP4 framework performs data harvesting, extract- ing and recording relevant statistics from the component pro- grams, reducing the occurrence of errors and inconsistencies being introduced by manual record keeping. MSD has imple- mented an interface in AutoDep that accepts uploads of har- vest data ﬁles and uses them to pre-ﬁll forms that would otherwise have to be completed manually by the depositor. We are also using AutoDep as a delivery platform for extra data and annotations that are generated during curation, mak- ing the deposition process richer and more useful to the depos- itor. Examples of the generated data that are returned to the depositor include quaternary structure assessments, structure *To whom correspondence should be addressed. Tel: +44 1223 494 646; Fax: +44 1223 494 468; Email: sameer@ebi.ac.uk The Author 2006. Published by Oxford University Press. All rights reserved. The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org