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www.wwpdb.org. September 7, 2007. Agenda. Welcome and introductions Accomplishments Remediation rollout summary Toward the future Break Matters arising Incorrect structures Executive session Feedback to wwPDB Set next meeting date.

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Wwpdb 1175755

www.wwpdb.org

September 7, 2007


Agenda
Agenda

  • Welcome and introductions

  • Accomplishments

  • Remediation rollout summary

  • Toward the future

    Break

  • Matters arising

    • Incorrect structures

  • Executive session

  • Feedback to wwPDB

  • Set next meeting date


Wwpdb achievements october 2006 september 2007
wwPDB AchievementsOctober 2006 - September 2007

  • Continued growth of archive

  • Website updates

  • Publications and presentations

  • Time-stamped archive

  • Remediation rollout

  • Annotation document

  • One stop shop: NMR, cryoEM



Pdb entry processing
PDB entry processing

  • 1-1-2000 10,997 entries in PDB

  • Today 10-Jul-2007 44,578 entries in PDB

    Size now is 4 times larger than when the 3 sites started

  • In 1999, 2361 entries were deposited

  • In 2006, 7282 entries were deposited

    We handle more than 3 times as many entries per year with less staff – and all wwPDB sites produce high quality annotated PDB entries

    No current backlog of unprocessed entries


Time stamped copies of the archive
Time-stamped copies of the archive

  • 57 Gbytes of data for 2006, released January 2, 2007

  • 68 Gbytes of data for July 2007 snapshot

  • Both include

    • PDB format entries

    • mmCIF format entries

    • PDBML format entries

    • Experimental data

    • Dictionary, schema, and format documentation


Outreach
Outreach

  • wwPDB website

  • Discussion forums

  • NMR Task Force

  • Publications

  • Professional society meetings


Joint publications
Joint publications

  • Nucleic Acids Research, 35: D301 (2007)

    • The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

  • Nature Structure Molecular Biology, 14:354 (2007)

    • Reply to: Building meaningful models of glycoproteins

  • Nature Biotechnology, 25: 854 (2007)

    • Response to “Overhauling the PDB”

  • Methods in Molecular Biology, in press

    • Data deposition and annotation at the wwPDB

  • Structural Bioinformatics 2nd Edition, in press

    • The wwPDB


Interactions since october 2006
Interactions since October 2006

  • Exchange visits

    • MSD/RCSB PDB (4)

    • PDBj/RCSB PDB (1)

    • PDBj/BMRB (2)

    • BMRB/RCSB PDB (1)

  • Phone conference with site directors-twice a year

  • VTC’s among staff

    • BMRB/RCSB PDB twice a month (ADIT-NMR)

    • MSD/RCSB PDB twice a week (annotation procedures, remediation)

    • RCSB PDB/PDBj and BMRB/PDBj on necessary occasions

  • Email among staff

    • MSD/RCSB PDB ~2 per day

    • PDBj/RCSB PDB ~2 per day


New initiatives
New initiatives

  • One stop shop for NMR data and models

  • One stop shop for electron microscopy maps and models (NIH-funded)


Recommendations from 2006 wwpdbac report
Recommendations from 2006 wwPDBAC report

  • Implement the recommendations from November 19-20 2005 modeling workshop (Berman et al.Structure 14, 1211-1217)

    • Models phased out October 16, 2006

  • Rollout remediated data to superusers by December 31, 2006; to all users by July 1st 2007; Provide access to PDB formatted files following the most current format.

    • Superusers had access to data November 2006, all users in April 2007


Recommendations from 2006 wwpdbac report1
Recommendations from 2006 wwPDBAC report

  • Work with SAXS community to create appropriate representation of these data, and circulate progress reports to the Committee as appropriate

    • Not done

  • Expand the four character PDB ID codes before the number of depositions reaches 400,000

    • Number of available PDB ID codes has been increased by allowing IDs to start with a character

  • Develop and present a formal recommendation to the wwPDBAC regarding the purview of the PDB at our September 2007 meeting in Princeton, NJ

    • In process


Recommendations from 2006 wwpdbac report2
Recommendations from 2006 wwPDBAC report

  • Coordinate with the wwPDBAC to obtain formal letters of support when seeking funding; establish a coordinated plan to both educate and lobby funding agency representatives; establish a charitable organization to serve as a conduit for receipt of both grant funding and gifts from pharmaceutical and biotechnology companies, involving individual Committee members as needed.

    • Funding Representatives Round Table Discussion



Key drivers
Key drivers

  • Chemistry and nomenclature

  • Sequence and taxonomy

  • Citations

  • Viruses


Iupac nmr and the pdb atom nomenclature and nmr restraints
IUPAC, NMR, and the PDBAtom nomenclature and NMR restraints

John L. Markley


History of the nmr led requested remediation of hydrogen atom nomenclature
History of the NMR-led requested remediation of hydrogen atom nomenclature

  • When BMRB was established in the late 1980’s, it adopted the IUPAC atom nomenclature recommendations from Biochemistry 9, 3471-3479, 1970

  • At that time, we noted that NMR structures being deposited in the PDB did not adhere to these recommendations (particularly for H-atoms; e.g. HB1/HB2 instead of HB2/HB3), and I brought this to the attention of the director of the PDB at Brookhaven with the request that it be remedied

  • A group of NMR spectroscopists led by Kurt Wüthrich worked with the NMR community to develop recommendations for the deposition of NMR structures; all agreed that the prior IUPAC recommendations be maintained (Pure & Appl. Chem., 70, 117-142, 1998)

  • Over the years, wwPDB Task Force on NMR has pushed strongly for remediation of atom nomenclature


Accomplished atom nomenclature remediation
Accomplished: atom nomenclature remediation atom nomenclature

  • Nomenclature in PDB now matches that in BMRB

  • The single format will avoid confusion and errors

  • All discrepancies have been resolved in the remediated files, with the minor exception of atoms at the C-terminus

    IUPAC-IUBMB-IUPAB wwPDB

    H'' HXT

    O' O

    O'' OXT

    • Since these atoms are not observed by NMR spectroscopists, we do not consider this to be a problem

    • We plan to write an addendum to the IUPAC-IUBMB-IUPAB “Recommendations” for submission to Pure & Appl. Chem. to formalize these as “accepted atom designators”


Remediation of nmr structure files
Remediation of NMR structure files atom nomenclature

  • Required the linking of structure files and restraint files

  • Atom names, residue numbers and chain identifiers needed to be updated

  • Remediation of restraint files required the unpacking, parsing, and regularization of legacy information contained in PDB “MR” files into the “NMR Restraints Grid”


Nmr restraints grid development
NMR Restraints Grid development atom nomenclature

BMRB, University of Wisconsin-Madison, USA

MSD, European Bioinformatics Institute, Hinxton, UK

Department of Computer Sciences/Condor Project, University of Wisconsin, USA

Department of NMR Spectroscopy, Utrecht University, The Netherlands

Centre for Molecular and Biomolecular Informatics, Radboud University, The Netherlands


Nmr restraints grid development1
NMR Restraints Grid development atom nomenclature

PDB MR files are converted into NMR-STAR

NMR-STAR file and the corresponding PDB coordinate file are parsed; the information is connected inside the CCPN framework; and the results are written out as NMR-STAR files; converted restraint files are filtered to remove redundant restraints

Files made available in the NMR Restraints Grid with access from links in each corresponding PDB entry

NMR restraint data files with atom nomenclature corresponding to remediated PDB data files will be available by the end of 2007


Current state of the nmr restraints grid
Current state of the NMR Restraints Grid atom nomenclature

  • Grid contains 3583 entries with a total of 3,882,595 parsed restraints

  • 3583 entries out of 6508 in PDB have restraints

  • Database is updated continuously as new PDB entries are released that have associated NMR restraints


Recent agenda items considered by the wwpdb nmr task force
Recent agenda items considered by the wwPDB NMR Task Force atom nomenclature

  • Strongly recommend that restraints be mandatory for all NMR depositions to the PDB

  • Commissioned the development of procedures for representing uncertainty in NMR structures and for specifying the single model meant to be most representative of the structure

  • Task Force should write an article for J. Biomol. NMR on its recommendations for data representation and submission of experimental data

  • It was suggested that the Task Force begin to discuss validation issues




Most structural genomics centers regularly provide restraints but the overall average is low
Most structural genomics centers regularly provide restraints, but the overall average is low

Number of NMR structures deposited

247

Percent of deposited structures with restraints

1127

880

Structural genomics center


Remediation rollout
Remediation rollout restraints, but the overall average is low

Helen M. Berman


Remediation scope and statistics
Remediation: scope and statistics restraints, but the overall average is low

  • All primary citations verified (45K)

  • Sequences & taxonomy updated for 61K sequences

  • Ligand stereochemistry and nomenclature for 13M monomers and 170K non-polymer molecules

  • Symmetry and coordinate transformations for 280 virus entries

  • 10814 diffraction source & beamline updates

  • ~1000 miscellaneous uniformity issues


Remediation process
Remediation process restraints, but the overall average is low

  • Corrections contributed and reviewed by all wwPDB members

  • Corrections on the archival mmCIF data files tracked in a version tracking system (CVS)

  • New PDBx/mmCIF, PDBML-XML, and PDB format data files produced

  • Validated by each wwPDB group

  • Staged public testing began January 2007

  • Iterative corrections based on external comments made through July 2007

  • Remediated archive released August 1, 2007


Remediation supporting infrastructure
Remediation-supporting infrastructure restraints, but the overall average is low

  • Internal (wwPDB) CVS archive remediation data files

  • Internal (wwPDB) rsync distribution site for remediated data files

  • Early tests of web, rsync, & ftp distribution sites for dictionaries, PDB, mmCIF, and XML data files

  • Complete wwPDB ftp site for remediated data and dictionaries updated with remediation corrections and weekly PDB updates

  • 200K CVS remediated data file updates

  • 1M+ remediated file updates to support testing and distribute from January 2007 - present


Checking the remediated files
Checking the remediated files restraints, but the overall average is low

Haruki Nakamura


Different checks
Different checks restraints, but the overall average is low

  • References to external databases

  • Data processing consistency checks

  • PDBML/XML validation

  • Database loads

  • User-contributed diagnostics


References to external databases
References to external databases restraints, but the overall average is low

  • Sequence and taxonomy (UniProt)

  • Primary Citations (PubMed)


Data processing consistency checks
Data processing consistency checks restraints, but the overall average is low

  • Covalent geometry and stereochemistry

  • Compliance with wwPDB Chemical Component Dictionary

    • Molecular and stereochemical assignment

    • Atom and residue nomenclature

  • Compliance with PDB Exchange Dictionary

    • Data types, controlled vocabularies, parent-child relations

  • External tools such as WhatIF


Pdbml xml schema validation
PDBML/XML schema validation restraints, but the overall average is low

  • Version control

  • Data type consistency

  • Data ranges

  • Controlled vocabularies

  • Referential integrity

  • XPath traversal of PDBML data hierarchy


Database loads
Database loads restraints, but the overall average is low

  • Diagnostics obtained from loading remediated data into existing database systems

    • Relational databases used by MSD-EBI and RCSB PDB

    • XML database used by PDBj


User contributed diagnostics
User-contributed diagnostics restraints, but the overall average is low

  • Batch checking of remediated files by Phenix revealed consistency issues with alternate conformations - Ralf Grosse-Kunstleve

  • Batch checking for inconsistent linkages and missing residues by docking software - Tommy Carstensen

  • Nomenclature - Tom Goddard & Chimera Group

  • Sequence and assembly diagnostics - Roland Dunbrack

  • Relational data integrity diagnostics - Dan Bosler

  • Nomenclature and experimental details - Clemens Vonrhein

  • Many specific issues related to chemical assignments, disorder, and nomenclature


Looking toward the future
Looking toward the future restraints, but the overall average is low

Kim Henrick


Annotation project
Annotation project restraints, but the overall average is low

  • Standardize annotation rules and policies among wwPDB sites

  • Document annotation rules and policies

  • Create venue to update annotation rules and policies as necessary


Annotation project1
Annotation project restraints, but the overall average is low

How did we get there?

  • Review and discussion of each PDB field by email and VTC

  • Document written and reviewed by all staff

  • Final review by site directors

  • Software compliant to new annotation procedures implemented

  • Tested software and trained annotators

  • Published document on web (January 2007)


Annotation document
Annotation document restraints, but the overall average is low

  • Specification of ALL fields in PDB file

  • Clarification of policies

    • Assignment of PDB IDs

    • Release of files and information

    • Changes to entries

  • Clarification of data representation

    • Chain ID for all atoms in the file

    • Multi-model representation for alternate conformation or disorder

    • Chimeras

    • Microheterogenity


Pdb ids and dois
PDB IDs and DOIs restraints, but the overall average is low

  • Credit for a PDB entry in CVs

  • Used as a reference in publications

    • http://dx.doi.org/10.2210/pdb4hhb/pdb

See also

DOIs for Biological Databases

Philip E. Bourne,

CrossRef 7th Annual Meeting,

1 November 2006

Cambridge, MA


Outstanding issues
Outstanding issues restraints, but the overall average is low

  • Microheterogeniety

  • Disorder

  • Large structures


Wwpdb and software developers
wwPDB and software developers restraints, but the overall average is low

  • ACA 24th July 2007 meeting in Salt Lake City

  • “Future Challenges for the PDB: What should the PDB be doing in 2015?”

  • Attended by software developers and wwPDB staff


July 24 meeting
July 24 meeting restraints, but the overall average is low

  • Technical discussions

    • TLS

    • Multiple models

    • Large structure

      • demand for one file per structure

    • Microheterogeneity

    • Twinning

      • George Sheldrick, Paul Adams and Garib Murshudov produce a draft of the PDB format to describe twinning and to represent the data in HKLF

  • Procedural outcomes

    • Yearly developer meeting

    • Editorial board to assist in difficult annotation problems

    • Ongoing electronic forum


Toward a single processing tool
Toward a single processing tool restraints, but the overall average is low

  • This weekend – wwPDB retreat with contributors from RCSB PDB Rutgers and UCSD, BMRB, PDBj, and EBI-EMBL

  • Task – come to agreement to pool resources to produce a single deposition tool and design of new processing pipeline


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