D288 Nucleic Acids Research, 2006, Vol. 34, Database issue quality metrics using electron density calculations (where structure factors are provided for X-ray entries) and detailed heterogen dictionaries. The UK-based eHTPX initiative (2) aims to unify the pro- cedures of protein structure determination into a single inter- face from which users can initiate, plan, direct and document their experiment either locally or remotely. As a partner in this initiative, the MSD is co-ordinating the development of com- mon data models that cover all stages from protein production through to structure solution and data deposition (http://www. ebi.ac.uk/msd-srv/docs/ehtpx/lims/) (3). The above data model is now being implemented as a fully functional Labor- atory Information Management System (LIMS) designated PIMS (http://www.pims-lims.org/). This forms part of a UK BBSRC-funded initiative that is working with EU projects and is based on the earlier HALX (4) and MOLE (5) applications. The BIOXHIT (http://icarus.embl-hamburg.de/bioxhit/) initi- ative forms a complimentary effort involving the MSD and CCP4 to deﬁne meta-data dictionaries for data exchange that will be implemented as XML schema to automate structure solution software pipelines. These initiatives will develop a framework to facilitate the tracking of data from target selec- tion through to deposition of the coordinates in the wwPDB. Similar mechanisms for data harvesting and deposition have been developed by the CCPN project (6), in which MSD is a consultative partner. The MSD group is also working with the EM community to develop a database for EM volume data and a deposition system for this data. The EM work is progressing with our involvement in the ‘3D-EM’ Network of Excellence funded within Research Framework Programme 6 of the European Commission (http://www.3dem-noe.org/). These close ties between the MSD and these two communities mean that we are well placed to bring together the three parallel efforts in structural biology, leveraging expertise from all three realms in the development of a new, uniﬁed data deposition architecture. Such a framework will allow us to perform rigorous checks and validations of deposited data, thereby improving the quality of the ﬁnal archives and ensur- ing accuracy for users of the data. AutoDep AutoDep version 4 (http://www.ebi.ac.uk/msd-srv/autodep4/) is a complete rewrite of the original AutoDep system, which was inherited from the ﬁrst deposition system, written at BNL during the early days of the PDB. The new application main- tains a superﬁcial similarity to the old AutoDep tool, in order to ensure an easy transition for users from the legacy system, but is a completely new implementation, using a Java servlet framework and XML as a data storage and interchange format. The system is highly customizable, owing to the system of ﬂexible XML-based dictionaries that deﬁne all aspects of the user interface and internal data formats. The new system includes various features that improve the quality of the ﬁnal data which are deposited into the PDB. The interface deﬁnitions include validation patterns that are auto- matically applied to user-supplied data as they are entered, allowing a ﬁrst round of data validation to be applied even as data are entered into the system. Once deposition is complete, but before submission, a suite of analysis programs are run, providing a further layer of validation for structures. Major problems in the uploaded coordinates are often identiﬁed at this stage of the deposition process, allowing the depositor to correct their data themselves, usually without intervention from AutoDep maintainers. Once the deposition is complete the entry is curated by the EBI staff. Allowing more rigorous and more detailed valida- tions to be performed on the deposited coordinates, the cura- tion process also allows us to return additional, value-added data to the depositor. Our hope is to encourage depositors to submit PDB entries before completion of the accompanying journal article, so that the deposition process becomes an additional analysis step, data from which can be included in the structure description. An example of the extra data that are derived, rather than being added by the depositor, is secondary structure information: the PDB uses standard programs to generate secondary structure records, ensuring consistent and uniform deﬁnitions are used throughout the archive. We also run a complex structural analysis that suggests the putative quaternary structure of the molecule in the crystal, the so-called PQS assembly (7). For X-ray entries where experi- mental data are deposited along with coordinates, we run an in- house version of the Uppsala Electron Density Server (8) and the CCP4 program SFCHECK (9). These allow us to verify that the supplied structure factors are those used to determine the structure as well as providing an additional measure of the quality of the structure in the form of the real-space R-factor and correlation coefﬁcients. Further checks on the structure are devoted to verifying the sequence of the PDB entry, through consideration of a residue-by-residue mapping to the UniProt sequence database (10), similar in nature to that available through the Structure Integration with Function, Taxonomy and Sequence (SIFTS) initiative (11). The sequence mapping allows us to validate several values in the PDB entry, such as the source organism for example, as well as the sequence itself. Depositors are notiﬁed of differences between the sequence of their structure and the corresponding UniProt entry, allowing them to correct sequence problems before the entry is released. Future developments in AutoDep will include data from other MSD services, such as MSDfold (12), which identiﬁes released PDB entries which exhibit a similar fold. An MSDfold query would permit us to show SCOP and CATH domain information for the new structure, further enhancing the range of information that is returned to the depositor during deposition. ELECTRON MICROSCOPY DATABASE The Electron Microscopy Database (EMDB) contains 3D volumes of biological macromolecules, determined by cryo- electron microscopy (13,14). Volumes are deposited by the cryo-EM community using the EMDep tool (http://www.ebi. ac.uk/msd-srv/emdep/), a system equivalent in scope to Auto- Dep. Since EMDep was launched in June 2002 we have received depositions of EM data from a wide variety of experi- ments, including tomography, icosahedral viruses, ribosomes and chaperonins. EMDep is a ﬂexible system for users to input complex macromolecular volume information into a databank in an interactive manner. The system leverages the knowledge