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John Westbrook Rutgers, The State University of New Jersey
www.wwpdb.org
The PDB and experimental data
Workshop on Metadata for raw data from X-ray diffraction and other structural techniques
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Overview
§ Current PDB audience and growth § Range of PDB primary ‘experimental metadata’ § Challenges for data acquisition and deposition
across the PDB view of the structural biology data pipeline
§ How we are addressing these challenges
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Protein Data Bank (PDB) § Single global repository for macromolecular
structure data (now >111K entries!)
§ Archival database - Users depend directly on the PDB; Other Databases present PDB contents
§ Our Users: Structural and Computational Specialists, Biophysicists, Biochemists, Biologists, Industrial Scientists, Educators, Students, and the General Public
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Worldwide Protein Data Bank
§ Ensures data are freely available § Data Centers
§ RCSB PDB (Research Collaboratory for Structural Bioinformatics)
§ PDBj (Osaka University) § PDBe (EMBL-EBI) § BioMagResBank (University
Wisconsin, Madison) § Institutional agreement § Formalized procedures for
deposition, validation, metadata representation, and annotation
§ Each data center provides unique delivery services
a
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PDB Depositors >800 new entries/month
RCSB PDB 347 million
PDBe 100 million
PDBj 58 million
PDB Users FTP and RSYNC Download TrafDic in 2014: 505 million downloads
Growing Number of PDB Depositions
As of 2014, ~50% increase in the number of global depositions since 2008
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Total Number of Annual Depositions
Projected Annual Depositions
Year
# of Entries
Archive Growth
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Increasing Complexity
Number of entries with peptide-‐like inhibitors/antibiotics released per year
Year Year
# of Entries
# of Entries
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Primary Experimental Content
…at the beginning of the
PDB pipeline
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Sample Details • Sample composition • Chemical and molecular descriptions • Source, production details, biological role • Crystallization conditions • Specimen preparation details
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Data Collection Details
§ Instrumentation details § Sample handling and collection conditions § Data collection protocol
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Skip a few steps …
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Data Processing Steps
§ Summary statistics § Software tools § Processed data
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Processed Data in the PDB Repository
§ Structure factor data sets for ~89% of current X-ray entries
§ ~10K additional data sets containing § Derivative and multiple wavelength data sets § Intermediate phasing data § Map coefficients § Unmerged intensities
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PDB Data Acquisition
Model Easy Sample Harder
Go figure….
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New Deposition System
mmCIF/PDBx
End-to-end support for PDBx/mmCIF metadata
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Data Harvesting Site pdb-extract.wwpdb.org/
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Data Harvesting Site pdb-extract.wwpdb.org/
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Structure Factor Utilities sf-tool.wwpdb.org/
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Data Entry Forms
Minimize manual input using PDBx deposition format & PDB_EXTRACT
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Chemical Assignment
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Chemical Reference Data Chemical Component Dictionary
§ Library of all polymer and non-polymer chemical components in PDB § >20,000 chemical component definitions § 400 additional definitions of amino acid
protonation variants § ~700 new components released this year § ~1700 component definitions updated this year § Complimentary to the CCP4 monomer library
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Using the experimental data we collect…
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Leveraging Exp. Data in Quality Assessment
22
Gray – not modeled Green, yellow, orange, red – 0,1,2, 3 or more issues Red dot – poor fit to electron density
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Map/Model Fit
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Improving data acquisition …
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PDBx Deposition Working Group
PDBx Deposition Working Group Oct 8 2014 Workshop – EBI/Hinxton
wwPDB Deposition
PDBx Format in the Lab
Structure Determination
Pipeline
Round Trip
wwPDB Processing
and Annotation
PDBx Format in wwPDB ftp Archive
§ In 2011, charged with finding a “round trip” single format that can handle complex data not supported by the PDB file format
§ Consensus reached on using dictionary-driven PDBx format
§ Implementations delivered in January 2013 § Currently working on recommendations for
delivery of non-standard chemistry and reflection/intensity data in later 2015
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Recommendations Under Development
§ Improved organization and packaging of structure factor, intensity, phasing and map data
§ Controlled vocabulary of data set content types § Standard specifications for each data category § Improved linking between related data sets,
crystal samples, and refined models § Incorporation of unmerged intensities and map
coefficients § Comprehensive representation of chemical
topology and restraints
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Restoring the missing bits …
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Identifying Related Experimental Data
§ References to hosted data sets § DOIs for data sets § DOIs for related metadata § Text descriptions of data and metadeta
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We Live in a Distributed World … just a few examples
http://www.ebi.ac.uk/pdbe/emdb/ http://www.ebi.ac.uk/pdbe/emdb/empiar/
http://www.sasbdb.org/
http://www.bmrb.wisc.edu/
http://proteindiffraction.org/
http://tardis.edu.au/deposit/
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First Step Data Identification - Next Step Federation
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop Structure 23: 1156–1167 doi: 10.1016/j.str.2015.05.013
Federation of loosely coupled resources with well defined data exchange protocols based on shared metadata standards.
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Acknowledgements
Funding: NIGMS