http://www.ebi.ac.uk/msd
AutoDep 4.0A 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
AutoDep 4.0
A new generation structure deposition and archival tool developed at the MSD.
(http://www.ebi.ac.uk/msd-srv/autodep4/)
http://www.ebi.ac.uk/msd
AutoDep 4.0
InterfaceArchitectureHarvesting
Annotation/Value added data
http://www.ebi.ac.uk/msd
• 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)
http://www.ebi.ac.uk/msd
AutoDep 4.0 (Interface)
Incomplete
http://www.ebi.ac.uk/msd
AutoDep 4.0
InterfaceArchitecture
HarvestingAnnotation/Value added
data
http://www.ebi.ac.uk/msd
• 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.
AutoDep 4.0 (Architecture)
http://www.ebi.ac.uk/msd
AutoDep 4.0 (Architecture)
XSLT
Data XML
PDB File
http://www.ebi.ac.uk/msd
AutoDep 4.0 (Architecture)
Interface XML Autodep XML Schema
http://www.ebi.ac.uk/msd
AutoDep 4.0
InterfaceArchitectureHarvesting
Annotation/Value added data
http://www.ebi.ac.uk/msd
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.
http://www.ebi.ac.uk/msd
AutoDep 4.0 (Harvesting)
Harvest File Upload
http://www.ebi.ac.uk/msd
AutoDep 4.0
InterfaceArchitectureHarvesting
Annotation/Value added data
http://www.ebi.ac.uk/msd
AutoDep 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
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)
http://www.ebi.ac.uk/msd
AutoDep 4.0 (Annotation)
http://www.ebi.ac.uk/msd
Details of a heterogen new to the PDB
AutoDep 4.0 (Annotation)
http://www.ebi.ac.uk/msd
AutoDep 4.0 (Annotation)
http://www.ebi.ac.uk/msd
AutoDep 4.0 (Annotation)
http://www.ebi.ac.uk/msd
Future development plansAdditional 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 (Annotation)
http://www.ebi.ac.uk/msd
• 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.
AutoDep 4.0
http://www.ebi.ac.uk/msd
How to make it work togetherInclude 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
CCP4 and AutoDep 4.0
http://www.ebi.ac.uk/msd
• 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.
Conclusions
http://www.ebi.ac.uk/msd
FundingFunding