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