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Validation, Deposition and Structure Quality

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wwPDB

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• 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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• 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

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Validation

Ramachandran Outlier !!!! Stereochemical Outlier !!!

Phenylalanine

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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

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The Problem

Number of Structures Processed as of 1-July-20053564 in 2002; 5507 in 2004

Total Number of Structures in PDB as of 10-Oct-200516,972 in 2001; 33,065 in 2005

PDB doubled in less than 4 years

2002 2003 2004 2005 2001 2002 2003 2004 2005

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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

Annotation Staff

2002 2005

RCSB 9 8

PDBj 5 5

MSD 5 4

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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.

Lack of Validation

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Validate your structures….

• Ensure geometry and stereochemistry are acceptable.• Ensure the sequences for 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.

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The Deposition Sites

AutoDep4.0 - MSD

ADIT – RCSB, PDBj

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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

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AutoDep 4.0

• A structure deposition and archiving system.• Based on Java/XML technology.

http://www.ebi.ac.uk/msd-srv/autodep4

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1. Autodep will parse file headers for Refmac, CNS and X-PLOR and autofill many sections in the form.

2. Can also parse Refmac, Scala, Truncate and CNS harvest files and fill in information regarding refinement etc.

AutoDep 4.0

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Validate Structure

AutoDep 4.0

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AutoDep 4.0

Validation Report

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AutoDep 4.0

Validation Report

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AutoDep 4.0

Validation Report

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• 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…

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Annotation@MSD

• 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

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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.

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Annotation Reports

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Annotation Reports

Details of a heterogen new to the PDB

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Annotation Reports

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Annotation People

Jawahar

RichardAdamandia

Sameer

John

JawaharAbdelkrim

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In Summary

• 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.

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Any Questions ?

pdbhelp@ebi.ac.uk – PDB Depositions Help Desk

Telephone: +44-(0)1223-494697