EMBL-EBI Validation, Deposition and Structure Quality 3/15/2018 1
EMBL-EBI 3/15/2018 ww. PDB 2
EMBL-EBI Validation • 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] 3/15/2018 3
EMBL-EBI Validation • Identify potential problems with structure/data before deposition to the ww. PDB. • Identify issues with bad geometry/strereochemistry. • Ensure that the structure is of the highest acceptable quality before deposition to the ww. PDB. • Identify sequence conflicts/differences from published sequence databases (Uni. Prot). 3/15/2018 4
EMBL-EBI Validation Ramachandran Outlier !!!! Stereochemical Outlier !!! Phenylalanine 3/15/2018 5
EMBL-EBI Validation Some programs for Structure Validation before deposition: • Procheck http: //www. biochem. ucl. ac. uk/~roman/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/validation 1. cgi 3/15/2018 6
EMBL-EBI The Problem PDB doubled in less than 4 years Number of Structures Processed Total Number of Structures in PDB as of 1 -July-2005 as of 10 -Oct-2005 3564 in 2002; 5507 in 2004 16, 972 in 2001; 33, 065 in 2005 2002 3/15/2018 2003 2004 2005 2001 2002 2003 2004 2005 7
EMBL-EBI Annotation Staff PDB annotation involves processing submissions to prepare standardised PDB entries. It doesn’t involve Uni. Prot curation of adding literature data to entries. 2002 2005 RCSB 9 8 PDBj 5 5 5 4 Standardisation of entries includes, standard format: MSD § correct ligand chemistry § correct sequence identification § assignment of assembly information 3/15/2018 8
EMBL-EBI Lack of Validation § Considerable automation in both ADIT and Autodep 4 § 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. 3/15/2018 9
EMBL-EBI 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. 3/15/2018 10
EMBL-EBI The Deposition Sites Auto. Dep 4. 0 - MSD ADIT – RCSB, PDBj 3/15/2018 11
EMBL-EBI 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 3/15/2018 12
EMBL-EBI Auto. Dep 4. 0 • A structure deposition and archiving system. • Based on Java/XML technology. http: //www. ebi. ac. uk/msd-srv/autodep 4 3/15/2018 13
EMBL-EBI Auto. Dep 4. 0 1. Autodep will parse file headers for Refmac, CNS and XPLOR 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. 3/15/2018 14
EMBL-EBI Auto. Dep 4. 0 Validate Structure 3/15/2018 15
EMBL-EBI Auto. Dep 4. 0 Validation Report 3/15/2018 16
EMBL-EBI Auto. Dep 4. 0 Validation Report 3/15/2018 17
EMBL-EBI Auto. Dep 4. 0 Validation Report 3/15/2018 18
EMBL-EBI Auto. Dep 4. 0 can be YOURS… • 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. 3/15/2018 19
EMBL-EBI • 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 3/15/2018 20
EMBL-EBI 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. 3/15/2018 21
EMBL-EBI Annotation Reports 3/15/2018 22
EMBL-EBI Annotation Reports Details of a heterogen new to the PDB 3/15/2018 23
EMBL-EBI Annotation Reports 3/15/2018 24
EMBL-EBI Annotation People Richard Abdelkrim Adamandia Jawahar John Sameer 3/15/2018 25
EMBL-EBI In Summary • • Validate structures before deposition. Improve our efficiency by providing information. Use Auto. Dep 4. 0 in-house for validation and archiving Use our annotation reports for further analysis of your structure quality. 3/15/2018 26
EMBL-EBI Any Questions ? pdbhelp@ebi. ac. uk – PDB Depositions Help Desk Telephone: +44 -(0)1223 -494697 3/15/2018 27
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