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AutoDep 4.0 A data deposition and archival system Sameer Velankar. PDB Deposition. A ‘poor’ cousin of the structure determination process. Low priority and often seen as a necessary evil for facilitating publication of structure.
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AutoDep 4.0A data deposition and archival systemSameer Velankar
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.
PDB Deposition A new generation structure deposition and archival tool developed at the MSD. (http://www.ebi.ac.uk/msd-srv/autodep4/) AutoDep 4.0
AutoDep 4.0 Interface Architecture Harvesting Annotation/Value added data
AutoDep 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.
AutoDep 4.0 (Interface) Incomplete
AutoDep 4.0 Interface Architecture Harvesting Annotation/Value added data
AutoDep 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.
Data XML PDB File XSLT AutoDep 4.0 (Architecture)
Interface XML Autodep XML Schema AutoDep 4.0 (Architecture)
AutoDep 4.0 Interface Architecture Harvesting Annotation/Value added data
AutoDep 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.
AutoDep 4.0 (Harvesting) Harvest File Upload
AutoDep 4.0 Interface Architecture Harvesting Annotation/Value added data
AutoDep 4.0 (Validation) • Built-in structure validation • Validation Reports generated include standard geometry and stereochemistry checks in addition to format.
AutoDep 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 their password-protected deposition session.
AutoDep 4.0 (Annotation) Details of a heterogen new to the PDB
AutoDep 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. AutoDep Functionality • Accepting pdb_extract harvest files • Integration with CCPN.
AutoDep 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.
CCP4 and AutoDep 4.0 How to make it work together Include AutoDep as part of CCP4 distribution. • in-house data archival system • One step data deposition • Structure validation software • Could intergrate PISA, MSDfold CCP4 exports XML • One step data deposition using a link in ccp4i
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 AutoDep interface.
Funding Funding
