Title: www.wwpdb.org
1www.wwpdb.org
September 7, 2007
2Agenda
- Welcome and introductions
- Accomplishments
- Remediation rollout summary
- Toward the future
- Break
- Matters arising
- Incorrect structures
- Executive session
- Feedback to wwPDB
- Set next meeting date
3wwPDB 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
4Depositions since wwPDB establishment
5PDB 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
6Time-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
7Outreach
- wwPDB website
- Discussion forums
- NMR Task Force
- Publications
- Professional society meetings
8(No Transcript)
9Joint 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, 14354 (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
10Interactions 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
- VTCs 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
11New initiatives
- One stop shop for NMR data and models
- One stop shop for electron microscopy maps and
models (NIH-funded)
12Recommendations 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
13Recommendations 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
14Recommendations 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
15Remediation
16Key drivers
- Chemistry and nomenclature
- Sequence and taxonomy
- Citations
- Viruses
17IUPAC, NMR, and the PDB Atom nomenclature and
NMR restraints
18History of the NMR-led requested remediation of
hydrogen atom nomenclature
- When BMRB was established in the late 1980s, 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
19Accomplished atom nomenclature remediation
- 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
20Remediation of NMR structure files
- 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
21NMR Restraints Grid development
- 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
22NMR Restraints Grid development
- 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
23Current state of the NMR Restraints Grid
- 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
24Recent agenda items considered by the wwPDB NMR
Task Force
- 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
25Most X-ray structures are supported by structure
factors
26Less than half of NMR structures are supported by
restraint data
27Most 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
28Remediation rollout
29Remediation scope and statistics
- 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
30Remediation process
- 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
31Remediation-supporting infrastructure
- 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
32Checking the remediated files
33Different checks
- References to external databases
- Data processing consistency checks
- PDBML/XML validation
- Database loads
- User-contributed diagnostics
34References to external databases
- Sequence and taxonomy (UniProt)
- Primary Citations (PubMed)
35Data processing consistency checks
- 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
36PDBML/XML schema validation
- Version control
- Data type consistency
- Data ranges
- Controlled vocabularies
- Referential integrity
- XPath traversal of PDBML data hierarchy
37Database loads
- Diagnostics obtained from loading remediated data
into existing database systems - Relational databases used by MSD-EBI and RCSB PDB
- XML database used by PDBj
38User-contributed diagnostics
- 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
39Looking toward the future
40Annotation project
- Standardize annotation rules and policies among
wwPDB sites - Document annotation rules and policies
- Create venue to update annotation rules and
policies as necessary
41Annotation project
- 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)
42Annotation document
- 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
43PDB IDs and DOIs
- 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
44Outstanding issues
- Microheterogeniety
- Disorder
- Large structures
45wwPDB and software developers
- 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
46July 24 meeting
- 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
47Toward a single processing tool
- 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