Auto Dep 4 0 A data deposition and

Auto. Dep 4. 0 A data deposition and archival system Sameer Velankar http: //www. ebi. ac. uk/msd

PDB Deposition • A ‘poor’ cousin of the structure determination process. • Low priority and often seen as a necessary evil for facilitating publication of structure. • Lack of seamless integration between structure determination to deposition. • Low return for time invested for deposition. http: //www. ebi. ac. uk/msd

Structure Determination/Genomics Pipeline http: //www. ebi. ac. uk/msd

PDB Deposition Auto. Dep 4. 0 A new generation structure deposition and archival tool developed at the MSD. (http: //www. ebi. ac. uk/msd-srv/autodep 4/) http: //www. ebi. ac. uk/msd

Auto. Dep 4. 0 Interface Architecture Harvesting Annotation/Value added data http: //www. ebi. ac. uk/msd

Auto. Dep 4. 0 (Interface) • Secured with user-provided password. • Context dependent page generation. • Inline validation of input Data. • Multiple deposition options to save time and effort. http: //www. ebi. ac. uk/msd

Auto. Dep 4. 0 (Interface) Incomplete http: //www. ebi. ac. uk/msd

Auto. Dep 4. 0 Interface Architecture Harvesting Annotation/Value added data http: //www. ebi. ac. uk/msd

Auto. Dep 4. 0 (Architecture) • Based on java/XML technologies. • XML dictionaries govern the look of the deposition interface and define data items • XSLT transformations generate web pages and produce a valid PDB file from the XML data. • Easily modifiable for other deposition scenarios by changing the XML schema. • Web-services (SOAP) compatible. http: //www. ebi. ac. uk/msd

Auto. Dep 4. 0 (Architecture) Data XML PDB File XSLT http: //www. ebi. ac. uk/msd

Auto. Dep 4. 0 (Architecture) Interface XML Autodep XML Schema http: //www. ebi. ac. uk/msd

Auto. Dep 4. 0 Interface Architecture Harvesting Annotation/Value added data http: //www. ebi. ac. uk/msd

Auto. Dep 4. 0 (Harvesting) • • Many modern crystallography programs write out harvest files. Other programs write out PDB-style headers with refinement information. Autodep 4. 0 parses file headers for Refmac, CNS, SHELX and X-PLOR and fills up relevant sections on the deposition form. Can also parse Refmac, Scala, Truncate and CNS harvest files and fill in information regarding refinement etc. http: //www. ebi. ac. uk/msd

Auto. Dep 4. 0 (Harvesting) Harvest File Upload http: //www. ebi. ac. uk/msd

Auto. Dep 4. 0 Interface Architecture Harvesting Annotation/Value added data http: //www. ebi. ac. uk/msd

Auto. Dep 4. 0 (Validation) • Built-in structure validation • Validation Reports generated include standard geometry and stereochemistry checks in addition to format. http: //www. ebi. ac. uk/msd

Auto. Dep 4. 0 (Annotation) Various items of data are returned to the depositor following annotation by the Curation Team. This information is only accessible to the depositor in http: //www. ebi. ac. uk/msd their password-protected deposition session.

Auto. Dep 4. 0 (Annotation) http: //www. ebi. ac. uk/msd

Auto. Dep 4. 0 (Annotation) Details of a heterogen new to the PDB http: //www. ebi. ac. uk/msd

Auto. Dep 4. 0 (Annotation) http: //www. ebi. ac. uk/msd

Auto. Dep 4. 0 (Annotation) http: //www. ebi. ac. uk/msd

Auto. Dep 4. 0 (Annotation) Future development plans Additional Annotation Reports (by end of the year) – Structure Similarity using MSDFold. – Small Motif identification using MSDMotif. – Ligand-binding site analysis using MSDSite. Auto. Dep Functionality – Accepting pdb_extract harvest files – Integration with CCPN. http: //www. ebi. ac. uk/msd

Auto. Dep 4. 0 • Available free under license (GPL) for academic and industry use. • Easy to install and useful for in-house archiving before deposition to the PDB via the MSD interface. • In-house deposition produces a tar archive which can be uploaded to the public interface to complete deposition in minutes. • Includes Tomcat, Java for intranet use, plus structure validation software. • Produces formatted PDB file for in-house use. http: //www. ebi. ac. uk/msd

CCP 4 and Auto. Dep 4. 0 How to make it work together Include Auto. Dep as part of CCP 4 distribution. – – in-house data archival system One step data deposition Structure validation software Could intergrate PISA, MSDfold CCP 4 exports XML – One step data deposition using a link in ccp 4 i http: //www. ebi. ac. uk/msd

Conclusions • Flexible and Extensible (Java/XML technology) • Provides an in-house structure archiving and validation system. • Can be adapted to a SOAP service for SG pipelines with minimal effort. • Mechanisms in place to return useful information via the Auto. Dep interface. http: //www. ebi. ac. uk/msd

Funding http: //www. ebi. ac. uk/msd