autodep 4 0 a data deposition and archival system sameer velankar n.
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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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pdb deposition
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 deposition1

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

AutoDep 4.0

Interface

Architecture

Harvesting

Annotation/Value added data

autodep 4 0 interface
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 01

AutoDep 4.0

Interface

Architecture

Harvesting

Annotation/Value added data

autodep 4 0 architecture
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.
autodep 4 02

AutoDep 4.0

Interface

Architecture

Harvesting

Annotation/Value added data

autodep 4 0 harvesting
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 harvesting1
AutoDep 4.0 (Harvesting)

Harvest File Upload

autodep 4 03

AutoDep 4.0

Interface

Architecture

Harvesting

Annotation/Value added data

autodep 4 0 validation
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
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 annotation2
AutoDep 4.0 (Annotation)

Details of a heterogen new to the PDB

autodep 4 0 annotation4
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 04
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
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
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

Funding