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Validation, Deposition and Structure Quality

Validation, Deposition and Structure Quality. wwPDB. validation n 1: the act of validating; finding or testing the truth of something [syn: proof ] 2: the cognitive process of establishing a valid proof [syn: establishment ]. Validation.

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Validation, Deposition and Structure Quality

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  1. Validation, Deposition and Structure Quality

  2. wwPDB

  3. validation n 1: the act of validating; finding or testing the truth of something [syn: proof] 2: the cognitive process of establishing a valid proof [syn: establishment] Validation

  4. Identify potential problems with structure/data before deposition to the wwPDB. Identify issues with bad geometry/strereochemistry. Ensure that the structure is of the highest acceptable quality before deposition to the wwPDB. Identify sequence conflicts/differences from published sequence databases (UniProt). Validation

  5. Validation Ramachandran Outlier !!!! Stereochemical Outlier !!! Phenylalanine

  6. Some programs for Structure Validation before deposition: Procheck http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html Biotech Validation Suite: http://biotech.ebi.ac.uk:8400/ WHATCHECK: http://swift.cmbi.ru.nl/gv/whatcheck/ JCSG Validation:http://www.jcsg.org/scripts/prod/validation1.cgi Validation

  7. The Problem PDB doubled in less than 4 years Number of Structures Processed as of 1-July-2005 3564 in 2002; 5507 in 2004 Total Number of Structures in PDB as of 10-Oct-2005 16,972 in 2001; 33,065 in 2005 2001 2002 2003 2004 2005 2002 2003 2004 2005

  8. Annotation Staff • PDB annotation involves processing submissions to prepare standardised PDB entries. • It doesn’t involve UniProt curation of adding literature data to entries. • Standardisation of entries includes, standard format: • correct ligand chemistry • correct sequence identification • assignment of assembly information

  9. Lack of Validation • Considerable automation in both ADIT and Autodep4 • However, increasing problems with depositors depending upon the annotation process to reveal problems in validation. • Many submissions involve re-refinement after deposition and annotation processing and re-submission of coordinates. • This requires considerably more work for annotation staff. • Both submissions tools not primarily designed for re-submissions of coordinates which arrive by email. • At MSD, turn-around for processing is slowing down.

  10. Ensure geometry and stereochemistry are acceptable. Ensure the sequencesfor all chains in your structure agree with a published sequence database source. Ensure you have validated your structure factors against a service like the EDS (http://eds.bmc.uu.se/) Deposit well before the release deadline or publication. Provide as much as information as possible in order that others may use your structure. Validate your structures….

  11. The Deposition Sites AutoDep4.0 - MSD ADIT – RCSB, PDBj

  12. Depositions Full deposition site from June 1999 ~20% of all submissions via the EBI. Partnership with RCSB and PDBj for a single PDB. All EBI processed data at release date are sent to RCSB for central distribution. Depositions started June 2002

  13. AutoDep 4.0 • A structure deposition and archiving system. • Based on Java/XML technology. http://www.ebi.ac.uk/msd-srv/autodep4

  14. AutoDep 4.0 • Autodep will parse file headers for Refmac, CNS and X-PLOR and autofill many sections in the form. • Can also parse Refmac, Scala, Truncate and CNS harvest files and fill in information regarding refinement etc.

  15. AutoDep 4.0 Validate Structure

  16. AutoDep 4.0 Validation Report

  17. AutoDep 4.0 Validation Report

  18. AutoDep 4.0 Validation Report

  19. Available free under license (GPL) for academic and industry use. Easy to install and use for in-house archiving before deposition to the PDB via the MSD interface. Includes Tomcat, Java for intranet use, plus structure validation software. Produces pretty PDB file for in-house use. AutoDep 4.0 can be YOURS…

  20. Authentication of source That the protein is from human and not rabbit, for example ! Authentication of structure Comparison of structure against raw data. Geometry and Stereochemistry. Provide results back to depositor. Validation of correct methodology used Whether X-Ray, NMR, EM or Theoretical Model. Conformity to standards Follows PDB format specifications Error checks Consistency checks - to identify simple typos Homo sapiens and not Homo sapien (single human?). Outlier detection - to identify suspect records Annotation@MSD

  21. Annotation Reports 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.

  22. Annotation Reports

  23. Annotation Reports Details of a heterogen new to the PDB

  24. Annotation Reports

  25. Richard Adamandia Jawahar Abdelkrim John Sameer Annotation People Jawahar

  26. Validate structures before deposition. Improve our efficiency by providing information. Use AutoDep4.0 in-house for validation and archiving Use our annotation reports for further analysis of your structure quality. In Summary

  27. Any Questions ? pdbhelp@ebi.ac.uk – PDB Depositions Help Desk Telephone: +44-(0)1223-494697

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