data management in the info@rcsb.org
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History of the PDB1970s
Community discussions about how to establish a PDBCold Spring Harbor meeting in protein crystallographyPDB established at Brookhaven (October 1971; 7 structures)
1980s Number of structures increases as technology improvesCommunity discussions about requiring depositionsIUCr guidelines establishedNumber of structures deposited increasesIndependent biological databases established – e.g., the NDB
1990smmCIF project completedStructural genomics beginsPDB moves to RCSB
2000sRCSB PDB renewedwwPDB established
PDB MissionPDB Mission
To provide the most accurate, well-annotated To provide the most accurate, well-annotated
data about macromolecular structure in the data about macromolecular structure in the
most timely and efficient way possible to most timely and efficient way possible to
facilitate new discoveries and advances in facilitate new discoveries and advances in
sciencescience
Structure Determination PipelineStructure Determination Pipeline(X-ray)(X-ray)
Hypothesis Driven Target
SelectionCrystallomics
DataCollection
StructureDetermination
Isolation, Expression,Purification,Crystallization
DataDeposition
DataRelease
Publication
System for Data Collection and System for Data Collection and Archiving Archiving
Depositor
ReportsFinal Files
DatabaseLoader
DataViews
MAXIT Validation
MetadataDictionaries
ADITAutoDepInput Tool
Data
Data Processing System Data Processing System Features Features
Different dictionaries without software changes
Simple customization of both functionality and content
Automatically scales with changes in content
Can be distributed to multiple deposition sites
Reference data and standard nomenclature (ERFs)
Data Content Data Content of Each PDB Entryof Each PDB Entry
1970’s1970’s Name, source, reference, resolution, Name, source, reference, resolution,
sequence,secondary structure, crystal data, coordinates, sequence,secondary structure, crystal data, coordinates, unstructured remarksunstructured remarks
1990’s1990’s Name, source, reference,resolution, Name, source, reference,resolution, refinement details, refinement details,
data collection and processing details,symmetry details, data collection and processing details,symmetry details, biological unit information, missing residues, related biological unit information, missing residues, related entriesentries, sequence, , sequence, ligand and ionsligand and ions, secondary structure, , secondary structure, crystal data, coordinates, crystal data, coordinates, few unstructured remarksfew unstructured remarks
Annotation and ValidationAnnotation and Validation ADIT ADIT
Reviewing, adding, correcting entry informationReviewing, adding, correcting entry information
MaxitMaxit File format conversionsFile format conversions
Blast Automation Tool resultsBlast Automation Tool results
Validation Server ReportsValidation Server Reports
Ligand Depot, ChemDrawLigand Depot, ChemDraw
RasMol for VisualizationRasMol for Visualization
PubMed, Citation Tracker, Citation Tool PubMed, Citation Tracker, Citation Tool
Extending Data Dictionaries for Extending Data Dictionaries for DepositionDeposition
X-ray X-ray
Structure determination data itemsStructure determination data items
http://deposit.pdb.org/mmcif/sg-data/xstal.htmlhttp://deposit.pdb.org/mmcif/sg-data/xstal.html
NMRNMR
Structure determination data itemsStructure determination data items
http:// deposit.pdb.org /mmcif/sg-data/nmr.htmlhttp:// deposit.pdb.org /mmcif/sg-data/nmr.html
Protein ProductionProtein Production
http:// deposit.pdb.org /mmcif/sg-data/protprod.htmlhttp:// deposit.pdb.org /mmcif/sg-data/protprod.html
Deposition Xray/NMR/EM by Deposition Xray/NMR/EM by yearyear
Deposition of X-ray, NMR & EM structures by year
0
500
1000
1500
2000
2500
196919711973197519771979198119831985198719891991199319951997199920012003
Year
X-ray
NMR
EM
Cryo-EM Dictionary ProposalCryo-EM Dictionary ProposalBiochemicalPreparation
em_sample_support
em_sample_preparation
em_solution_composition
em_array_formation
EM SpecimenPreparation
em_vitrification
em_stain
em_cryo_stain
em_embedding_agent
EM Data Collection
em_microscope
em_imaging
em_detector
em_electron_diffraction
em_image_scans
em_micrographs
em_electron_diffraction_phase
em_electron_diffraction_pattern
Structure Analysisem_3d_fitting
em_3d_fitting_list
em_classes
em_refinement
em_fsc_curve
Image Processing
em_3d_reconstruction
em_particle_picking
em_singleparticle_selection
em_particle_picking_list
em_filament_selection
em_filament_reconstruction
SampleDescription
em_assembly
em_entity_assembly
em_entity_assembly_list
em_icos_virus_shells
em_virus_entity
em_filaments
em_single_particle
em_2d_crystal
MARCH2005
New categoriesrecommended at
the Oct 2004 workshopare in pink
Target Registration DatabaseTarget Registration DatabaseTargetDB • http://targetdb.pdb.org/TargetDB • http://targetdb.pdb.org/
All targets downloadable in XML (~51,000 Targets)All targets downloadable in XML (~51,000 Targets) Targets downloaded from 18 centers weeklyTargets downloaded from 18 centers weekly Target search by:Target search by:
Sequence (FASTA), project target ID, project site, status (selected, Sequence (FASTA), project target ID, project site, status (selected, cloned, expressed, … in PDB), update date, protein name, source cloned, expressed, … in PDB), update date, protein name, source organismorganism
Report output in HTML, FASTA, and XMLReport output in HTML, FASTA, and XML Integrates PDB entry sequences (~55,600 sequences)Integrates PDB entry sequences (~55,600 sequences) Includes PDB pre-release sequence dataIncludes PDB pre-release sequence data Provides links to related sequence databasesProvides links to related sequence databases Open to all Structural Genomics projectsOpen to all Structural Genomics projects Summary reports of target or project progressSummary reports of target or project progress
Protein Expression Purification and Protein Expression Purification and Crystallization Database (PepcDB)Crystallization Database (PepcDB)
Extends content of TargetDB Extends content of TargetDB
All protocols for cloning, expression, purification are All protocols for cloning, expression, purification are stored and are searchablestored and are searchable
Reports provide links to status history, related Reports provide links to status history, related protocols, project, sequence and domain databasesprotocols, project, sequence and domain databases
Incremental Assembly
PepcDB
TargetDB
Target and Protocol Tracking
Target Tracking
PDB
Merging and integration
Target Selection
Samplepreparation
DataCollection
DataProcessing
StructureSolution
Refinement
Protocols
Tracking, Assembling and Tracking, Assembling and Archiving DataArchiving Data
Reengineered Web SiteReengineered Web Sitepdbbeta.rcsb.orgpdbbeta.rcsb.org
Built on curated dataBuilt on curated data
Three-tier architectureThree-tier architecture Database tierDatabase tier Middle tierMiddle tier Presentation tierPresentation tier
Feedback from usersFeedback from users Help deskHelp desk Usability engineeringUsability engineering Focus groupsFocus groups
Went into public beta testing in July 2004Went into public beta testing in July 2004
Navigation and Query
Persistent Navigation Bar
Site Search HierarchicalMenu Items
PersistentSearch Box
Integrated Help(Context-sensitive)
GettingStarted
Worldwide PDB (wwPDB)Worldwide PDB (wwPDB) RCSB (Research Collaboratory for Structural RCSB (Research Collaboratory for Structural
Bioinformatics)Bioinformatics) PDBj (Osaka University)PDBj (Osaka University) Macromolecular Structure Database (EBI)Macromolecular Structure Database (EBI)
To ensure that PDB files remain in a single archive To ensure that PDB files remain in a single archive to best serve the worldwide community of depositors to best serve the worldwide community of depositors and usersand users
http://www.wwpdb.org/
AcknowledgementsAcknowledgements
Operated by the Research Collaboratory of Structural Bioinformatics
Supported by:
NIGMS
RCSB-PDB Team
RCSB PDB Team: Ken Addess, Helen M. Berman, Wolfgang F. Bluhm, Phil Bourne, Kyle Burkhardt, Li Chen, Sharon Cousin, Jim Croker, Nita Deshpande, Shuchismita Dutta, Zukang Feng, Lew-Christiane Fernandez, Judith L. Flippen-Anderson, Gary Gilliland, Rachel Kramer Green, Vladimir Guranovic, Shri Jain, Ann Kagehiro, Charlie Knezevich, Andrei Kouranov, Kevin Lwinmoe, Jeff Merino-Ott, Irina Persikova, Suzanne Richman, Melcoir Rosas, Kathryn Rosecrans, Bohdan Schneider, Wayne Townsend-Merino, Susan Van Arnum, Elizabeth Walker, John Westbrook, Alice Xenachis, Huanwang Yang, Jasmin Yang, Christine Zardecki, Cindy Zhang
www.pdb.org • info@rcsb.org
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