Embed Size (px)
Citation preview
November 6, 2009
www.wwpdb.org
November 6, 2009
Agenda
Summary Overview Haruki Nakamura
Common Deposition and Annotation Tool
Martha Quesada
Method- and Molecule-specific Activities
John MarkleyGerard Kleywegt
Policy and New Ventures
PDB Journal
Helen Berman
Matt Day
November 6, 2009
Summary Overview
Haruki Nakamura
Worldwide Protein Data Bank
www.wwpdb.org
November 6, 2009
wwPDBAC 2008 Recommendations Establish validation procedures for X-ray and NMR
– X-ray Task Force draft report; NMR Task Force established Establish recommendations for additional data deposition and release
requirements– Policy document updated
Work with SAXS/SANS community– First report completed
Definition of purview of the PDB– For approval at this meeting
Establish feasibility of chemical shift depositions– Implementation plan
Independent funding for wwPDB– wwPDB Foundation established
Develop wwPDBAC membership plan– Done
Establish EM Task Force– First EMDB AC Meeting held March 2009
Broaden wwPDBAC to include China and India– Associate Members: Zihe Rao (China) and Manju Bansal (India)
November 6, 2009
wwPDB October 2008 - September 2009
New Leadership PDBe-Gerard Kleywegt Funding stable at 4 sites Continued growth of archive Increased use of data PDB Archive Version 3.15 released: archival
snapshots Further coordination of FTP and web updates Common Tool Project underway Establishment of wwPDB Foundation Continued outreach
November 6, 2009
Funding RCSB PDB competitive renewal funded by NSF
– January 2009 - December 2013
PDBe competitive grant from Wellcome Trust– December 2009 - November 2014– Additional new permanent EMBL posts-from 2013: stable core of at least 15 permanent
posts (from 6 in 2008!)
PDBj competitive renewal funded by JST (Japan Science & Technology Agency)– April 2006 - March 2011: Current program– April 2011 - March 2014: A new funding system for life-science databases is planned
BMRB competitive renewal funded from the National Library of Medicine– September 2009 – August 2014 (parent grant)– September 2009 – August 2011 (administrative supplement – US recovery act funding)– September 2009 – August 2011 (competitive renewal – US recovery act funding)
November 6, 2009
*
By experimentaltype
By deposition and processing site*(projected)
(*8322)
0
10002000
3000
4000
50006000
7000
8000
9000
19721973197419751976197719781979198019811982198319841985198619871988198919901991199219931994199519961997199819992000200120022003200420052006200720082009
X-ray
NMR
EM
PDB Depositions
November 6, 2009
Increase of PDB data depositions from Asia and Oceania regions
China
Hong KongTaiwan
Australia
India
New Zealand
November 6, 2009
PDB Downloads
0
10,000,000
20,000,000
30,000,000
40,000,000
50,000,000
60,000,000
70,000,000
2007-082007-092007-102007-112007-122008-012008-022008-032008-042008-052008-062008-072008-082008-092008-102008-112008-122009-012009-022009-032009-042009-052009-06
* *1st month after version 3.0/3.1 files
released
1st month after version 3.15 files
released
November 6, 2009
PDB FTP Traffic (July 2008 - June 2009)
RCSB PDB200 milliondata downloads
PDBe37 milliondata downloads
PDBj14 milliondata downloads
November 6, 2009
Remediation Rollout
Complete PDB File Format Contents Guide Version 3.20 released (Sep 2008)
PDB format version 3.15 files released (March 2009)– New records/remarks: describe models, ligands and zero
occupancy atoms/residues – Enhancements: assemblies, SITE records, chain IDs,
database references (including taxonomy id, PubMed, DOI IDs) added for all files
– Various corrections (including sequence, beamline, wavelength, atom connectivities, atom nomenclature, mmCIF consistency)
– Missing remarks restored
November 6, 2009
Common Tool for Deposition and Annotation
Manage increased data load without an increase in resources
Create global deposition and annotation tools Proof of concept delivered July 2009 First test system due June 2010
November 6, 2009
wwPDB Foundation
Will enable funding for wwPDBAC meetings and outreach activities
Bylaws created Paperwork filed
November 6, 2009
Outreach Joint publications Meeting posters,
exhibit booths, and presentations – eChemInfo, EMBO
Practical Course: Macromolecular Crystallography, Biophysical Society, Experimental Biology, Biocuration Meeting, ISMB/ECCB, Protein Society, ACA, ACS, AsCA
Website Helpdesk
At AsCa’09 Beijing
Se Won Suh
Mitchell Guss
November 6, 2009
Formalized Internal Communications Phone conferences among site directors
Regular exchange visits
Weekly VTC’s among staff– Common Tool
– EM
– NMR
– Data annotation
Electronic reporting (validation, structure
assignments, FTP updates, etc.)
wwPDB Retreat 2009
November 6, 2009
Common Deposition and Annotation (D&A) Tool
Martha Quesada
Worldwide Protein Data Bank
www.wwpdb.org
November 6, 2009
2007 wwPDB RetreatWhat strategic objectives should we start to address now to meet our goals in the next 5 – 10 years?
IMPACT
CO
ST
November 6, 2009
Drivers and Opportunities wwPDB Common D & A Tool Project New deposition types: multiple methods and new data New validation procedures Need to support higher throughput Limited resources for new development and maintenance Process inefficiencies
– Redundant tools in use: AutoDep and ADIT, data harmonization required
Good collaborations among sites– Possibility of sharing of workload– Precedent for common tools for NMR and EM
November 6, 2009
Inflection Point
Business as usual
Ready for today
New capabilities
Change the game
Time
Usage,Impact
Decision to come together as the wwPDB in developing the tools that will support the shared functions of the wwPDB for the next 10 years
November 6, 2009
wwPDB Common D&A Tool ProjectThe goal is to implement a set of common deposition and annotation processes and tools that will enable the wwPDB to deliver a resource of increasingly high quality and dependability over the next 10 years.
The tools will address: the increase in complexity and experimental variety of submissions and the increase in deposition throughput
The processes and tools will maximize the efficiency and effectiveness of data handling and support for the scientific community
November 6, 2009
Project Scope Common deposition interface and processing
– Coordinates (x,y,z) regardless of experiment origin (X-ray, NMR, EM)– NMR restraints, chemical shifts– X-ray structure factors– 3D-EM maps
Data processing: Validation Tools– Fit of model to data– Coordinates for polymers and ligands– NMR Restraints– Structure factor validation– EM map validation
Partly developed by External Task Forces
To be integrated over time
November 6, 2009
Assumptions & Constraints
Functional requirements– Deposition tool must handle all current, agreed upon data entry and
report formats from the user community– All data elements covered within the PDB annotation manual must
be included
Technical requirement– Design will enable flexibility for growth and evolution– Technical level reasonable standard, not bleeding edge or declining– Design must enable integration with community data capture
November 6, 2009
For example Deposition will capture all currently deposited
experimental data for each method The tool will support all data formats and validation
requirements for all deposition types The system will allow for workload balancing during
deposition
November 6, 2009
Potentially novel designs require early
experimentation
Potentially novel designs require early
experimentation
Common D&A Project Characteristics Large and complex – Break into smaller bits
Distributed developers – Establish development controls and communication
Some requirements well understood – Policies in place
Some requirements evolvingIteration 1
Iteration 2
Iteration n
Increment deliveredReview lessons learned
Etcetera…
1. 2.
5.
3.
4.6.
1. 2.
5.
3.
4.6.
1. 2.
5.
3.
4.6.
November 6, 2009
Modern Requirements Analysis
Process (workflow) driven: As is vs. To be– What exactly do we actually do?– Analyze current processes– What works and where are the opportunities?– What would be the ideal process?
Alignment of requirements to workflow– Functional requirements
calculations, decision trees, reports, communication– Data flow requirements– Technical (strategic and tactical) requirements
November 6, 2009
Project Phases, Structure and Roles
Steering Committee– Governance– Milestone reviews and guidance
Concept Team – Initial requirements and design
Core Team (Functional leaders)– Plan and manage the project
Project Teams – Design, develop and test component solutions– Deliver the solution
Develop & Test
Delivery
Initiation
Concept
ReqmtDesign
November 6, 2009
Communication and Coordination
Among all of the project stakeholders– Inward facing– Outward facing
Between distributed functional and development groups
November 6, 2009
Initiation
Concept
Steering Committee (wwPDB Directors)October 2007 Set project Project Goal, Scope,
Assumptions and Constraints, initial timelines
Approves project at each milestone
Concept TeamNovember 2007 Objectives, strategies and metrics Stakeholder analysis & risk
assessment New system requirements Concept process maps
Approved May 08
November 6, 2009
Objectives & Strategies Improve data quality beginning at data capture
– Provide for interactive feedback and value to the depositors during the deposition process
– Employ community-driven validation methods
Improve efficiency – Standardization, automation and more flexible data sharing
Improve existing tools – Use “best of breed” existing tools where possible– Free resources to redevelop/develop new common tools
Enable system maintenance and evolution – system modularity
November 6, 2009
Initiation of Design and PlanningThe Core Team, representing the functional groups and sites, leads the project through design and implementation in conversation with the Steering Committee
RCSB PDB: John Westbrook, Jasmine Young; PDBe: Tom Oldfield, Sameer Velankar, Jawahar Swaminathan; BMRB: Steve Mading, Eldon Urlich; PDBj: Takanori Matssura
Develop & Test
ReqmtDesign
November 6, 2009
Project Team: Distributed
Delivery
Subject and technical experts from all sites
ReqmtDesign
Develop & Test
Quarterly face-to-face meetings
Weekly VTC team working meetings
On-going teleconferences and email
Shared web-based document and code management tools
November 6, 2009
Key Design ElementsModular construction through an API
•Reuse of “best of breed” existing tools; redevelop tools as time and need dictate. •Enable system maintenance and evolution
Improved workflow efficiency for faster processing•Workflow automation - workflow engine and manager
Improved collaboration•More flexible data sharing
Proposed technical design and deliverables reviewed and approved by the Steering Committee
November 6, 2009
July 2009Technical Design Proof Of Concept Application Programming Interface: API
– “wrapped” application functionality Faster processing through improved efficiency
– workflow automation implementation Improved collaboration
– Snapmirror tested
Potentially novel designs require early
experimentation
Potentially novel designs require early
experimentation
Python Core API LayerPython Core API Layer
C/C++ Apps
C/C++ Apps
Fortran Apps
Fortran Apps RDBMSRDBMS
Other ServicesOther
Services
Workflow EngineWorkflow Engine
November 6, 2009
January 2010 - Production Deliverable
Implementation of an annotation module
With GO BACK functionality
Expansion of workflow proof of concept
Implementation of the API using existing functionality and the “Master Format”
Introduction of “Go Back” functionality
Improved user interface
Integrated with existing workflows.
November 6, 2009
Project Progress July 2008: Initiate Design and Development Planning
(Core Team) Nov 2008: Define Data Model Requirements (Project
Team Meeting), Flesh out Design elements March 2009: Finalized design elements and initiate
development of “proof of concept” July 2009: Deliver design “proof of concept” January 2010: First production deliverable
2009 2010
Concept
RequirementsDesign
DevelopmentTest
Delivery
4Q 2007 2008 2011
Initiation
November 6, 2009
wwPDB Common D&A ToolProject Timeline Going Forward
Concept Define deliverables Initial design Process definition Data model definition
Requirements elaboration Data flow documentation Technical Design
Data Sharing & Replication API, Master Format Automated Workflow
Technical Proof of Concept Development of initial production deliverable• Communication design
production deliverables
D&A system delivery
Initiation
Concept
2009 20104Q 2007 2008 2011
RequirementsDesign
DeliveryDevelopmentTest
November 6, 2009
Ultimate Project Deliverables For Depositors
– Interactive and informative deposition interface– Value added validation input and annotation during deposition– Faster processing
For Annotators– Improve efficiency, freeing time for more advanced annotation
Improved quality early in the process Automation of appropriate processing steps Best of breed tools Expanded functionality
– Enable system maintenance and evolution through system modularity
For Data Users– Higher Quality Archive
November 6, 2009
Method and Molecule-specific Activities
John Markley
Gerard Kleywegt
Worldwide Protein Data Bank
www.wwpdb.org
November 6, 2009
NMR
November 6, 2009
NMR Update
Remediated NMR restraints project is near NMR Validation Task Force established
– First meeting held Sept 21, 2009, in Paris, France
Implementation plan for Chemical Shifts requirement in progress
Status of SMSDep
November 6, 2009
NMR Validation Task Force: Charge Advise on validation of new NMR data depositions Provide a report for the wwPDB AC Provide recommendations for structure validation criteria and
tools– Tools and procedures recommended should be freely
available and simple to install and maintain so users can easily use in own laboratories
– Tools should not be used as a basis to “reject” structures, but to flag potential problems for the depositor/user to be aware of
– Recommendations should be assembled into a “white paper” for publication
– Recommendations should be targeted to software developers, depositors, journal editors, and PDB users
November 6, 2009
NMR Validation Task ForceCommittee MembersGaetano Montelione (Co-Chair, Rutgers)Michael Nilges (Co-Chair, Institut Pasteur)Ad Bax (NIH)*Peter Guentert (University Frankfurt)Torsten Herrmann (CNRS/ENS Lyon)Jane Richardson (Duke University)Charles Schwieters (NIH)Geerten Vuister (Radboud University)*David Wishart (University of Alberta)
* Notes on the Paris meetingAd Bax and Eldon Ulrich were unable to attend
the meetingJurgen Doreleijers attended as a substitute for
Geerten Vuister
Meeting Observers
Naohiro Kobayashi (PDBj-BMRB)
John Markley (NMR VTF Organizer)
Randy Read (Chair, X-ray VTF)
Eldon Ulrich (BMRB)*
Wim Vranken (PDBe)
John Westbrook (RCSB PDB)
November 6, 2009
NMR VTF: Outcome of first meetingSeptember 21, 2009; Paris, France General consensus on the value of expanded NMR validation
for the scientific community. Consensus on coordination with X-ray VTF on common
validation issues. Requirements and available tools for validation were assessed
during the meeting. Areas targeted for further research: format consistency for
restraints, treatment of internal dynamics and ensemble averaging.
Website and mail archive created to support task force communication
November 6, 2009
Chemical Shifts: Progress in implementation
BMRB has been the primary deposition and processing site for NMR chemical shift (CS) data
Mandatory chemical shift and reference data items have been defined, and a prototype mandatory CS system is in place
wwPDB to perform minimal processing:– check format and sanity check at deposition– substitute explicit atoms for pseudo-atoms – maintain nomenclature correspondence during annotation
Data files are to be transferred to BMRB for further annotation PDB will release chemical shift files in NMR-STAR format along with
coordinate data files Download statistics for chemical shift data files will be be maintained
for BMRB (needed for grant reporting)
November 6, 2009
SMSDep
Deposition system is in place and accepting structures and associated NMR chemical shifts
Current policy is to accept data only for small peptides or nucleic acids (processing and annotation is carried out at PDBj-BMRB)
We need to monitor the level of activity to determine whether this site should be maintained
November 6, 2009
X-ray
November 6, 2009
wwPDB X-ray Validation Task Force Initial meeting
– April 14-16, 2008 EBI, Hinxton, UK– R. Read (Chair), P. Adams, A. Brunger, P. Emsley, R. Joosten, G.
Kleywegt, E. Krissinel, T. Luetteke, Z. Otwinowski, T. Perrakis, J. Richardson, W. Sheffler, J. Smith, I. Tickle, G. Vriend
Goal – Gather recommendations and consensus on additional
validation for PDB entries, and identify software applications for these validation tasks
– Provide code/algorithms for the validation-software pipeline
Preliminary Outcome– Candidate global and local validation measures were
identified – These measures were reviewed in terms of the
requirements of depositors, reviewers, and users
November 6, 2009
X-ray Validation Task Force:Next Steps May 2008 - September 2009: discussions (e-mail, Gordon
Conference) and report writing October 2009: Meeting to complete report during Cold Spring Harbor
Laboratory Crystallography Course November 2009: Report presented at wwPDBAC
wwPDB partners are pooling manpower to implement Task Force recommendations– One dedicated programmer to implement the validation-software
pipeline (Swanand Gore) Validation tools and procedures will also be incorporated in the new
wwPDB Common Deposition and Annotation system
November 6, 2009
wwPDB X-ray Validation Task Force Apply new knowledge of structure
– proteins, nucleic acids, carbohydrates, ligands
New opportunities from mandatory data– fit to data, quality of data, pathologies
Exploit new technologies– machine-readable annotation
Serve the different communities– users, depositors, editors/referees
November 6, 2009
Ramachandran revisited
November 6, 2009
Clashes and holes
November 6, 2009
One intuitive summary of quality
November 6, 2009
Members of X-ray VTF
Paul Adams Axel Brunger Paul Emsley
Roobie Joosten
Gerard Kleywegt* Eugene Krissinel
Thomas Lütteke
Zbyszek Otwinowski
Tassos Perrakis
Jane Richardson
Will Sheffler Janet Smith
Ian Tickle Gert Vriend Randy Read
November 6, 2009
SAXS/SANS
November 6, 2009
SAXS/SANS
Increase of SAS publications for structural biology– Higher intensity sources– Advances in data analysis
and modeling tools
Increase in number of deposition requests since 2005
Number of hits from simple search of publications by using protein structure and small angle scattering
November 6, 2009
SAXS/SANS: Current Status
Two types of models– Atomic model with a directed sequence
– Dummy residue model
41 structures have been deposited since 1998– 7 Model 1
– 2 Model 2 (withdrawn)
– 32 are between Model 1 and 2 (chain of C)
Model 1
Model 2
November 6, 2009
wwPDB proposed requirements for a SAXS/SANS PDB entry
Model is derived and fully defined by the experimental data Model is a folded chain of residues with directionality COMPND, SOURCE, SEQRES and external sequence reference
(DBREF) are included x,y,z coordinates per atom. Cα or P model allowed Has acceptable geometry (bond-length, bond-angle, torsion-angle, non-
bonded contacts, etc.) Experimental and refinement details recorded in appropriate REMARK
records Parameters directly derived from the scattering profile should be supplied
and appropriately recorded (radius of gyration, Dmax in distance distribution function, mass, etc.)
Reduced 1D experimental profile Family of models should be superimposed
November 6, 2009
SAXS/SANS: Next Steps
Create a SAXS/SANS Task Force to advise the wwPDB– Which if any SAXS/SANS models should be in
PDB?– Template for PDB file – Validation standards
November 6, 2009
Electron Microscopy
November 6, 2009
Electron Microscopy
Collaborative project between RCSB PDB, PDBe, and Baylor-NCMI is funded by NIH, BBSRC, and EMBL
Unified tool for collecting model coordinates and map files in a one-stop shop
Merge deposition and annotation with PDB as part of Common Tool by 2011
November 6, 2009
EM Coordinate and Map Depositions
November 6, 2009
EMDatabank.org
Joint map + coordinate deposition service Emdatabank.org: news, EM software list, information about
dictionaries, conventions, FAQ page, community links EMSEARCH: search by ID, author, sample type, keyword,
deposition date EMViewer: simple map viewer
November 6, 2009
EMDB Annotation 1 EBI annotator in 2002 1 RCSB PDB annotator added in 2008 Joint deposition of map and model enables
joint validation Annotation document has been written Remediation underway to improve uniformity of
maps and header XML files Letters sent to journals about deposition
requirements
November 6, 2009
EM Navigator Service provided by PDBj: Search for EM data through EMDB with the corresponding PDB data Views of EM 3D structures with or without the relating atomic structures in PDB as movies and by molecular viewers
Will test the newly remediated EM map files so as to ensure the quality of these files
November 6, 2009
Next steps
Community input on modeling criteria for EM maps-First meeting January 2010
Set up EM Task Force to set deposition and validation standards for deposition
Set requirements for EM for the Common Tool project
Target date for incorporation of EM maps into the PDB-2011
November 6, 2009
Complex Chemistry of Peptide-Like Molecules in the PDB: Antibiotics and Inhibitors
November 6, 2009
Challenges
Inclusion of non-standard amino acid, nucleotides, or other chemical groups in sequence
Non-linear (cyclic or branched) sequences Microheterogeneity (some cases) Non-uniform annotation of the same molecule
in different PDB entries Lack of annotation regarding the source and
function of these molecules
November 6, 2009
Solutions
Analyze and classify– Groups antibiotics and inhibitors into polymeric molecules or
single components
Chemical Component Dictionary updates Remediate files Establish rules for future processing Create Peptide Reference Dictionary
November 6, 2009
Peptide-Like Molecules: Inhibitors Combined (single component) (406)
Retained as polymer (350)
Split to polymer (23)
FFRCK; PPACK IISubcomp: DPN PHE ARG 0QE
PepstatinIVA VAL VAL STA ALA STA1 2 3 4 5 6
LeupeptinAce-Leu-Leu-Argal1 2 3 4
November 6, 2009
Peptide-Like molecules: Antibiotics
Split for clear and correct representation (180)
Actinomycin D (non-ribosomal product)THR DVA PRO SAR MVA PXZ THR DVA PRO SAR MVA1 2 3 4 5 6 7 8 9 10 11
Thiostrepton (gene product)I A S A S C T T C I C T C S C S S1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
November 6, 2009
Peptide Reference Dictionary (PRD)
Initial research completed (summer interns) Checking and corrections (in progress) Information to be incorporated in remediated
files Dictionary to be made available to all
November 6, 2009
Status of Peptide-Like Molecules
Inhibitor remediations (RCSB PDB)
Antibiotic remediations (PDBe)
Expected release: Spring 2010
November 6, 2009
Policy Issues and New Ventures
Helen Berman
Worldwide Protein Data Bank
www.wwpdb.org
November 6, 2009
Molecules Accepted by wwPDB
Current Requirement: Polypeptide structures with 24 or more residues Polynucleotide structures with 4 or more
residues Polysaccharide structures with 4 or more
residues
November 6, 2009
Molecules Accepted by wwPDB
Proposed Requirement Polypeptide structures
– Gene products– Naturally-occurring non-ribosomally synthesized peptides – Peptidic repeat units of large fibrous polymers – Synthetic peptides of at least 24 residues unless there is a clear case
that it is of biological relevance
Polynucleotide structures – With 4 or more residues
Polysaccharide structures – With 4 or more residues
November 6, 2009
PDB Format Problems
Large structures not accommodated in current format– > 62 chains– 99999 atoms
Level of experimental detail Multiple models Non-homogeneous models Non-linear sequences (e.g., carbohydrates)
November 6, 2009
Proposal
Create a modified PDB format for ATOM and others records such that is possible to– calculate electron-density maps– validate of the model and its fit to the experimental data– continue or re-do the refinement
Meta data would be represented in PDBx Small group of key community members
would be consulted New format in place by Q4 2010
November 6, 2009
Status Code Clarification
Author Approval of Annotation
Report?
No Author Response &
No issues
No Author Response &
Entry has Issues &
Paper is published
No Author Response &
Entry has Issues &
No paper is published
RELRelease
immediatelyRelease after 3 weeks
Release with CAVEAT record upon electronic
publication of corresponding paper
Withdrawn 12 months after deposition
HPUBRelease upon
electronic publication
Release upon electronic publication
Release with CAVEAT record upon electronic
publication of corresponding paper
Withdrawn 12 months after deposition
HOLD
At most a year after deposition; entry is
released upon electronic
publication based upon journal policy
At most a year after deposition; entry may be released upon electronic publication based upon
journal policy
Release with CAVEAT record upon electronic
publication of corresponding paper
Withdrawn 12 months after deposition
November 6, 2009
Obsolete Entries Appears in entries that have been removed from main
distribution into ftp://ftp.wwpdb.org/pub/pdb/data/structures/obsolete/
It is PDB policy that only the principal investigator and/or the primary author who submitted an entry has the authority to obsolete it
OBSLTE indicates which, if any, new entries have replaced the entry that was obsoleted (SPRSDE)
Explanation for obsolete entries without replacement entry should be included in files
November 6, 2009
Fabricated Structures
Problem: A PDB entry is found to be fabricated
Proposed Action: If the author does not agree to OBSLTE the entry, the employer of the author may request that PDB entry be made OBSLTE. This request must be appropriately documented. The citation for the obsolete entry must be a published explanation of the circumstances that led to retraction of the paper(s) and associated PDB entry or entries.
November 6, 2009
Worldwide Protein Data Bank Foundation, Inc. Organized to benefit the public and to support and
ensure the functioning of the wwPDB AC Conducts the annual review meeting to ensure the
continued effectiveness of the collaboration Conducts seminars and workshops with the purpose
of educating the public and promoting the goals and activities of the wwPDB in curation, archiving, and disseminating the common data archive of biological macromolecules
Fundraising initiatives include journal and donations
November 6, 2009
Worldwide Protein Data Bank Foundation, Inc. Bylaws filed with the state of New Jersey Board of Trustees
– 4 members, one elected by each wwPDB site
Officers– Elected by the Board of Trustees– President, Secretary, Treasurer
November 6, 2009
Industrial Interactions
Increased interactions/collaborations with software companies: OpenEye, CCG, Schrodinger leading to improved data files
US-CSAR: Community Structure Activity Resource are collecting model and binding data from pharma. Refined structures will be sent to PDB
Europe-Innovative Medicines Initiative's Open Pharma Space may provide a source of industrial models
