The Protein Data Bank Swanand Gore amp Gerard Kleywegt PDBe EBI May 7 th 2010 910 am Macromolecular Crystallography Course Outline Structural Biology and Bioinformatics Databases in Structural Bioinformatics ID: 552456
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Slide1
Structure Databases:The Protein Data Bank
Swanand Gore & Gerard KleywegtPDBe – EBIMay 7th 2010, 9-10 am
Macromolecular Crystallography CourseSlide2
Outline
Structural Biology and BioinformaticsDatabases in Structural BioinformaticsProtein Data BankPDBeSlide3
Promise of Structural Biology
Basic researchInsights in biophysics of foldingInsights into EvolutionInsights into enzymatic catalysisApplicationsDesign of drug / antibody / epitope / pesticide / enzymes
Design of new materialsUnderstanding diseaseStructural bioinformaticsBig computational and informatics toolbox
Full of techniques to translate insights to applicationDatabases are a vital aspectSlide4
Sequence-Structure-Function
Sequence
Function
Prediction
Modelling
Determination
Archival / Retrieval
Classification
Structure
Searching
Mining
Comparison
Alignment
Design
EngineeringSlide5
A rich toolboxSlide6
Databases are central to structural bioinformatics pipeline
Primary StructuralDatabases
DetermineAnnotate
Align
CompareMine
Classify
Model
Predict
Secondary Structural
DatabasesSlide7
Databases help in Structure Determination
Dihedral preferencesRamachandran contoursSidechain rotamer librariesRNA backbone and puckersLikely ring conformations
Small-molecules (CCDC)Molecular replacementChoice of probe using homologyfragment-based MRValidation
Electron density server and PrEDS
Dunbrack
, R.L., Jr.
Rotamer
libraries in the 21st century.
Curr
.
Opin
.
Struct
. Biol. 12:431-440, 2002.
Jane S. Richardson et al (2008) "RNA Backbone: Consensus All-angle Conformers and Modular String Nomenclature (an RNA Ontology Consortium contribution)" RNA 14 :465-481
The Cambridge Structural Database: a quarter of a million crystal structures and rising, F. H. Allen, /Acta
Cryst./, B*58*, 380-388, 2002 S.C. Lovell et al. (2003) "Structure Validation by C
α Geometry: φ,ψ and Cβ Deviation." Proteins: Structure, Function and Genetics 50, 437-450.
Claude et al.
CaspR
: a web server for automated molecular replacement using homology modelling. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W606-9.
McCoy, A.J., Grosse-
Kunstleve
, R.W., Adams, P.D., Winn, M.D.,
Storoni
, L.C. and Read, R.J. (2007).
Phaser
crystallographic software.
J. Appl.
Cryst
.
40: 658-674.
Gubbi
et al. (2007)
Solving Protein Structures Using Molecular Replacement Via Protein Fragments, Lecture Notes In Artificial
Intelligence;.Vol
. 4578. 627.
GJ
Kleywegt
et al. (2004) "The Uppsala Electron-Density Server",
Acta
Crystallographica
, D60, 2240-2249 Slide8
Databases are vital to archiving structures!
Structures represent invaluable scientific insightsBut it is costly to solve a structureTime, effort, moneyOrganize and safe-keep painstakingly determined dataFormal mechanisms of arranging, searching, backing upWide-ranged access to invaluable repository without compromising data integrity
Very low cost of maintenance in comparison with the cost of content!Slide9
Databases are vital to archiving structures
“Database is a structured collection of data held in computer storage, often incorporating software to make it accessible in various ways”
Databases
Provide accessibility with safety and persistence
Provide context for your data against other data
Facilitate comparisons and data-mining
Primary structural databases
Experimental data and model coordinates
NDB,
wwPDB
, BMRB, CSD, EMDB
Secondary structural databases
Classification, function annotation
SCOP, EC2PDB, PALI, and many
many
more!Slide10
Databases / Archival / Retrieval
Formats of databasesFlat files (csv, tsv, columnar), supporting scriptsRelational (MySQL, Oracle): professional, indexed
AccessModes: read, write, edit, delete (PDB provides entry deposition mechanisms)Means: Download (wwPDB ftp), Command-line or GUI (SQL queries, Oracle desktop client), Web-based interfaces (
PDBeDatabase service)Access frequency
Schema design
Tables, primary keys, foreign keys, views….
Normal forms: avoid data repetition, inconsistenciesSlide11
Databases for Classification
Structural hierarchyCATHClass, Architecture, Topology, HomologySCOPClass, Fold, Superfamily, FamilyEnzyme hierarchy
EC-PDBOxidoreductase, ligase, lyase
, isomerase, hydrolase, transferase.
Functional ontologyGOAGene Ontology: Cellular component, Biological process, Molecular Function
Linked to structures via SIFTS
Christos A.
Ouzounis
et al. (2005)
Classification schemes for protein structure and function Nature Reviews Genetics 4, 508-519.
Andreeva
et al. (2007) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. 36:D419
Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium (2000) Nature Genet. 25: 25-29
Barrell
D. et al. (2009) The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucleic Acids Research 2009 37: D396-D403.Slide12
Databases for Comparison
Structural and structure-sequence alignmentsPhylogenyEvolutionary trace
Evolutionarily important residuesMapping onto structure
Mizuguchi
K, Deane CM, Blundell TL,
Overington
JP. (1998) HOMSTRAD: a database of protein structure alignments for homologous families.
Protein Science
7:2469-2471.
SISYPHUS - structural alignments for proteins with non-trivial relationships
Andreeva
et al,
Nucleic Acid Research Database Issue 2007, 35, D253-D259
Gowri
, V. S. Et al. (2003). Integration of related sequences with protein three-dimensional structural families in an updated Version of PALI database. Nucleic Acids Res. 2003 31: 486-488.
Bhaduri
A,
Pugalenthi
G,
Sowdhamini
R. PASS2: an automated database of protein alignments organised as structural
superfamilies
.
BMC Bioinformatics
. 2004, 5:35
DBAli
tools: mining the protein structure space. Marc A. Marti-
Renom
et al. Nucleic Acids Research, doi:10.1093/
nar
/gkm236
Whelan, S., P.I.W. de Bakker, & N. Goldman. (2003).
Pandit
: a database of protein and associated nucleotide domains with inferred trees.
Bioinformatics
19:1556-1563
The
Pfam
protein families
database:,R.D
.
Finn,et
al, Nucleic Acids Research (2010) Database Issue 38:D211-222
Morgan, D.H., D.M.
Kristensen
, D.
Mittleman
, and O.
Lichtarge
. ET Viewer: An Application for Predicting and Visualizing Functional Sites in Protein Structures. Bioinformatics. 2006 Aug 15;22(16):2049-50Slide13
Databases for Annotation
SNPsServant F. rt al (2002)
ProDom: Automated clustering of homologous domains. Briefings in Bioinformatics. vol 3, no 3:246-251
Marchler-Bauer A,et al CDD: specific functional annotation with the Conserved Domain Database.
Nucleic Acids Res. 2009 Jan;37(Database issue):D205-10Hulo N.,
Bairoch
A.,
Bulliard
V.,
Cerutti
L.,
Cuche
B., De Castro E.,
Lachaize C., Langendijk-Genevaux P.S., Sigrist
C.J.A. The 20 years of PROSITE. Nucleic Acids Res. 2007SitesBase
: a database for structure-based protein–ligand binding site comparisons , Nicola D. Gold and Richard M. Jackson, Nucleic Acids Research, 2006, Vol. 34, Database issue D231-D234
sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank, Esther Kellenberger
et al, J. Chem. Inf. Model., 2006, 46 (2), pp 717–727
Binding MOAD, a high-quality protein–
ligand
database. Mark L. Benson et al, Nucleic Acids Research 2008 36(Database issue):D674-D678
SNPeffect
v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs . Joke
Reumers
at al, Bioinformatics 2006 22(17):2183-2185
Domains
Active /
allosteric
sitesSlide14
Databases for Annotation
CREDO: A Protein-Ligand Interaction Database for Drug Discovery.Adrian Schreyer, Tom Blundell. Chemical Biology & Drug Design, Vol. 73, No. 2. (February 2009), pp. 157-167
BIPA: a database for protein–nucleic acid interaction in 3D structures. Semin Lee and Tom L Blundell, Bioinformatics 2009 25(12):1559-1560
PIBASE: a comprehensive database of structurally defined protein interfaces. Davis FP and Sali
A, Bioinformatics. 2005 May 1;21(9):1901-7.JAIL: a structure-based interface library for macromolecules. Stefan Günther
et al. Nucleic Acids Res. 2009 January; 37(Database issue): D338–D341
Elke
Michalsky
et al.,
SuperLigands
– a database of
ligand
structures derived from the Protein Data Bank, BMC Bioinformatics
2005, 6:122Voronoia: analyzing packing in protein structures. Rother K et al. Nucleic Acids Res. 2009 Jan;37(Database issue):D393-5.
CASTp: Computed Atlas of Surface Topography of proteins. Binkowski
et al. Nucleic Acids Res. 2003 Jul 1;31(13):3352-5.The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Craig T. Porter, Gail J. Bartlett, and Janet M. Thornton (2004)
Nucl. Acids. Res. 32: D129-D133.
Binding partners
Small molecule: TIMBAL, CREDO
Protein, DNA –
PiBase
JAIL, BIPA
Residues critical to enzyme mechanism
Surface properties, cavities:
V
oronoia
,Slide15
Databases of Analysis / Mining
Secondary structure: SSEPActive sitesOliva
et al (1997) An automated classification of the structure of protein loops. J Mol Biol 266 (4): 814-830.
SSEP: secondary structural elements of proteins , V. Shanthi, P. Selvarani, Ch.
Kiran Kumar, C. S. Mohire and K. SekarNucleic Acids Research, 2003, Vol. 31, No. 13 3404-3405
PepX
: a structural database of non-redundant protein-peptide complexes.
Vanhee
F et al., Nucleic Acids Res. 2010 Jan;38(Database issue):D545-51.
Baeten
L, et al. (2008) Reconstruction of Protein Backbones from the
BriX
Collection of Canonical Protein Fragments.
PLoS
Comput Biol
4(5): e1000083. doi:10.1371/journal.pcbi.1000083Bystroff C & Baker D. (1998). Prediction of local structure in proteins using a library of sequence-structure motifs.
J Mol Biol 281, 565-77.
LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Stuart AC et al., Bioinformatics. 2002 Jan;18(1):200-1.
PTGL—a web-based database application for protein topologies. Patrick May et al. Bioinformatics 2004 20(17):3277-3279; doi:10.1093/bioinformatics/bth367
Fitzkee
, N. C., Fleming, P. J, Rose G. D. (2005) The Protein Coil Library: a structural database of
nonhelix
,
nonstrand
fragments derived from the PDB.
Proteins.
58 (4): 852-4.
Protein-peptide interactions
Loop databases
Protein Coil Library
Protein Loop Classification
Loops in Proteins
Protein Topology Graph Library
Frequent structural motifsSlide16
Databases in Prediction
Oligomeric statePISA at PDBe3D coordinatesab-initio foldinghomology models
Possible binding partners and binding modessmall-molecule (PRECISE)protein-protein (ADAN)
Dynamics, conformational changesMolMovDBCellular location
LOC3D: annotate sub-cellular localization for protein structures. Nair R,
Rost
B., Nucleic Acids Res. 2003 Jul 1;31(13):3337-40.
MolMovDB
: analysis and visualization of conformational change and structural flexibility. Echols N et al., Nucleic Acids Res. 2003 Jan 1;31(1):478-82.
ADAN: a database for prediction of protein-protein interaction of modular domains mediated by linear motifs.
Encinar
JA et al., Bioinformatics. 2009 Sep 15;25(18):2418-24.
Epub
2009 Jul 14.
PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes .
Shu-Hsien
Sheu
et al., Nucleic Acids Research, 2005, Vol. 33, Database issue D206-D211
MODBASE, a database of annotated comparative protein structure models and associated resources. Ursula Pieper et al.,
Nucleic Acids Research
37, D347-D354, 2009.
Krissinel
E,
Henrick
K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. (2007) 372:774–797.
S. M. Larson .
Folding@Home
and
Genome@Home
: Using distributed computing to tackle previously intractable problems in computational biology. Mod Meth Comp
Biol
, R. Grant,
ed
, Horizon Press (2003)Slide17
Specialized databases with structures
MCSIS (GPCRs, Prions etc)CarbohydratesKEGG Glycans
Antibodies (
Abysis
)
Lysozymes
Abysis
: http://www.bioinf.org.uk/abysis/
Horn F.,
Vriend
G., Cohen FE. Collecting and harvesting biological data: the GPCRDB and
NucleaRDB
information systems. Nucleic Acids Res. 29:346-349 (2001)
LySDB
-
Lysozyme
Structural
DataBase
. Mohan KS et al.,
Acta
Crystallogr
D
Biol
Crystallogr
. 2004 Mar;60(Pt 3):597-600.Slide18
The Protein Data Bank
Unique primary databaseSingle archive of experimentally determined macromolecular (biopolymer) structures~ 65000 entriesDistributed onlineUpdated weeklyNumerous databases derived and enriched with PDB dataMany frontends- RCSB,
PDBe, PDBsum, OCA, MMDB, Jena, SIB“The PDB” is a flat-file archive
PDB formatted coordinate filesany experimental data when submittedSlide19
The Protein Data Bank
International EffortCurated by RCSB, PDBe,
PDBj, BMRBftp archive currently operated by RCSBSlide20
FTP traffic at PDB sites
RCSB PDB
200 million
data downloads
PDBe
37 million
data downloads
PDBj
14 million
data downloadsSlide21
The Protein Data Bank
When is a biopolymer PDB-worthy?PolypeptidesGene productsNon-ribosomalSynthetic peptides > 23 residuesUnless clearly biologically significant
Polynucleotides> 3 residuesSugars> 3 sugar residues
FibersOnly repeating unit depositedSlide22
Annual Growth of PDB
Primary databases differ
by magnitudes in size.
UniprotKB
107
protein sequences
GenBank
10
11
base pairs
10
8
gene sequences
< 10
5
structures
http://www.rcsb.org/pdb/statistics/contentGrowthChart.do?content=total&seqid=100
http://www.ncbi.nlm.nih.gov/Genbank/genbankstats.htmlhttp://www.ebi.ac.uk/uniprot/TrEMBLstats/Slide23
Annual Growth of PDB
Dominated by x-ray!
EM rising…Slide24
Redundancy in PDB(as in Nov’08)
Entries > 54,000Chains > 120,000Copies of a chain in same entryHomo-oligomersSame chains in different entriesDetermined by multiple labs
Determined under different conditionsComplexed with different partnersMutants
Chains < 8700 at seq.id < 30%Orthologs, paralogs are very similar
Using non-redundant chains from PDBPISCES serverWHATIF, CATH, SCOP, DALI sets
G. Wang and R. L.
Dunbrack
, Jr. PISCES: a protein sequence culling server.
Bioinformatics
, 19:1589-1591, 2003.Slide25
File formats at PDB
The .pdb formatHeaderRemarksexperimental setupRefinement detailsoligomeric state
deviations from expected geometryBiochemical entitiesBiopolymers, het groupsCoordinates3D model of the entity
Multiple coordinates for same entity can existsMODELs, altloc identifiers
Structure factors.cif fileSlide26
File formats at PDB
XML
mmCIFSlide27
The PDB format: header
123456789+123456789+123456789+123456789+123456789+123456789+123456789+123456789+HEADER RETINOIC-ACID TRANSPORT 28-SEP-94 1CBS
1CBS 2COMPND CELLULAR RETINOIC-ACID-BINDING PROTEIN TYPE II COMPLEXED 1CBS 3
COMPND 2 WITH ALL-TRANS-RETINOIC ACID (THE PRESUMED PHYSIOLOGICAL 1CBS 4COMPND 3 LIGAND) 1CBS 5
SOURCE HUMAN (HOMO SAPIENS) 1CBS 6
SOURCE 2 EXPRESSION SYSTEM: (ESCHERICHIA COLI) BL21 (DE3) 1CBS 7
SOURCE 3 PLASMID: PET-3A 1CBS 8
SOURCE 4 GENE: HUMAN CRABP-II 1CBS 9
AUTHOR G.J.KLEYWEGT,T.BERGFORS,T.A.JONES 1CBS 10
REVDAT 1 26-JAN-95 1CBS 0 1CBS 11
Column 1-6
Record type
Column 7-72 - human-readable, mostly
textual informationSlide28
The PDB format: coordinates
HETATM 1 C ACE A 0 4.279 14.829 14.190 1.00 19.08 C HETATM 2 O ACE A 0 3.706 14.098 15.038 1.00 20.62 O HETATM 3 CH3 ACE A 0 3.827 16.236 14.001 1.00 20.22 C
ATOM 4 N MET A 1 5.514 14.621 13.695 1.00 17.77 N ATOM 5 CA MET A 1 6.269 13.401 13.959 1.00 16.51 C
ATOM 6 C MET A 1 6.702 13.319 15.400 1.00 16.41 C ATOM 7 O MET A 1 7.036 12.248 15.870 1.00 15.38 O
ATOM 8 CB MET A 1 7.529 13.301 13.085 1.00 16.52 C ATOM 9 CG MET A 1 7.292 12.805 11.676 1.00 16.48 C
Atom nr
Residue type
Atom name
Chain name
Residue nr
“B-factor”
Occupancy
X, Y, Z coordinatesSlide29
Protein Data Bank in Europe
PDBeEuropean node of wwPDBStarted 1996 as MSD at EBIDeposition site since 1999Started EMDB in 2002PDBe operations
Handle deposition and annotation of PDB and EMDB entriesBuild advanced structure databasesBuild services for search, browsing, analysisLiaise with broader structural biology community
Coordinate with other databases e.g. UniprotFunding
PDBe
: Protein Data Bank in Europe. S.
Velankar
et al
.,
Nucleic Acids Research, doi:10.1093/
nar
/gkp916Slide30
PDBe Deposition and Annotation
ChecksIs format correct?Are biopolymer sequences in biochemical entities consistent with 3D models?Are hetero groups named correctly?Where all does model deviate from expected geometry?Record various types of information
Experiment: Method, conditions, data resolution, spacegroup, completeness etc.Sample: source, expression system, engineered etc.Refinement: program, target
AutoDep
Deposition
ToolSlide31
AutoDep provides valuable information to depositors
Validation of structure factorsEDS criteria
http://www.ebi.ac.uk/pdbe-xdep/autodep/index.jspSlide32
AutoDep provides valuable information to depositors
Heterogen summary and Validation against ideal representations of ligandsSlide33
AutoDep provides valuable information to depositors
Oligomeric state - PQS
Sequence-structure alignment
Uniprot
,
Pfam
,
InterproSlide34
AutoDep provides valuable information to depositors
Revisions, withdrawal, releaseRelease sequence-only immediatelyRelease coordinates immediatelyHold for 1 yearRelease after publicationCommunication with depositors
Help depositors understand and conform to PDB standardsDiscussing errorsSlide35
PDBe Services
PISA, SSM/ PDBeFold, PDBeMotif, PDBeChem, SIFTS, PDBeStatistics,
PDBeSearch, PDBeView
PDBe
ServicesSlide36
PDBe Services
PDBeView – the Atlas pages
http://www.ebi.ac.uk/pdbe-srv/view/Slide37
PDBe Services
PDBeFold (SSM): has my fold been seen before? Or is it novel!
PDB
???
E. Krissinel and K. Henrick
, Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions.
Acta
Cryst
. (2004). D60, 2256±2268.Slide38
PDBe Services
Why compare structures?Reveal conformational changesLigands, mutations, crystal packing, pH..Judge structural variabilityNMR ensembles, structure families
Discover common structural motifsIdentify foldInfer functionSequence-alignments do not work well for distant evolutionary relationships
Structures diverge much slowly than sequencesStructure improves quality of alignmentBetter inference of function, e.g. when active sites match well
PDBeFold
(SSM)
The relation between the divergence of sequence and structure in proteins.
Chothia
C,
Lesk
AM. EMBO J. 1986 Apr;5(4):823-6.Slide39
PDBe Services
PDBeFold (SSM) algorithm
H
1
S
1
S
2
S
3
S
4
H
2
H
1
H
2
H
3
H
4
S
1
H
5
H
6
S
2
S
3
S
4
S
5
S
6
S
7
Match SSE graphs to get initial alignment
Iterative expansion of C
a
-alignmentSlide40
PDBe Services
PDBeFold (SSM)
SSM can carry out genuine multiple structure alignment to reveal a motif common to a family of structuresSlide41
PDBe Services
PDBePISA
What is the likely biological assembly of a
given structure?
Can I learn about it from crystal-packing of chains?
PDB file (ASU)
Biological Unit
Crystal Symmetry
ASU
PISA
Generate possible assemblies
Rank according to free energySlide42
PDBe Services
PDBePISA
PDB entry 1P30A monomer?
Biological unit 1P30
Homotrimer
!Slide43
PDBe Services
PDBePISA
PDB entry 2TBVA trimer?
Biological Unit 2TBV
180-mer!Slide44
PDBe Services
PDBePISASlide45
PDBe Services
PDBePISA
PDB entry
1E94
2 Biological Units in 1E94:
A dodecamer and a hexamer!Slide46
PDBe Services
PDBeMotif
A very powerful
engine to
search PDB
Structure-sequence general searches
Chemical substructure
Predefined frequent motifs
Arbitrary secondary structure patterns
Φψ
patterns
Protein sequences
Prosite
motif,
Uniprot
, CSA accessionsRaw sequence
Regular expressionInteractions between
ligands
, protein
Seq
-distance between protein motifs
PDB header searches
Specialized searches
Envionment
around an interaction
Motif binding
Occurrence of a motif inside another
MSDmotif
: exploring protein sites and motifs. Adel
Golovin
and Kim
Henrick
.
BMC Bioinformatics 2008, 9:312Slide47
PDBe
ServicesPDBeMotif: which motif does my substructure bind often?
Staurosporine
Kinase
inhibitorSlide48
PDBe Services
PDBeMotif: which ligands and chemical fragments does my sequence motif bind?
Tyrosine protein
kinase
-specific active-site signature:
[LIVMFYC]-{A}-[HY]-x-D-[LIVMFY]-[RSTAC]-{D}-{PF}-N-[LIVMFYC](3)
Motif binding statistics
Chemical fragmentsSlide49
PDBe Services
PDBeMotif: how does a sequence motif look like in 3D?
Tyrosine protein
kinase
-specific active-site signature:
[LIVMFYC]-{A}-[HY]-x-D-[LIVMFY]-[RSTAC]-{D}-{PF}-N-[LIVMFYC](3)
Sequence hits
3D alignmentSlide50
PDBe Services
PDBeMotif: which sequences often host a Ramachandran path?
3D fragment
φ/
ψ sequence
-156/-155,-103/17,-134/161
Search
Sequence patternSlide51
PDBe Services
PDBeAnalysis: selections and statistics
Structure
Statistics
frequency plots on 1 or 2 properties of entries
Residue
Statistics
Choose residues and make frequency plots of a property
Choose residues in entry meeting certain filters, and plot their property
Atom
Statistics
Choose atom-sets in entries and plots distance, angle, dihedrals between them
Structure Selection
Create a subset of entries using various filters
Database Browser
Web-based SQL
query page to internal database
Geometric Validation coupled with 3D viewer
http://www.ebi.ac.uk/pdbe-as/pdbevalidate/Slide52
PDBe Services
PDBeAnalysis: selections and statistics
Resolution vs
Rfactor
CA1-CA2-CA3-CA4
Torsion distribution
Low res
High resSlide53
PDBe Services
PDBeAnalysis: geometric validation
Table and plot of geometric checks
Phi-psi, chi, omega, B-value,bonds, angles,
chiralitiesAstexViewer
coordinated with plotsSlide54
PDBe Community Work
X-rayCCP4 software: MMDB, PISA, SSM, harvestingValidation Task ForceNMRCCP-NMR softwareValidation task force
EMValidation and standardsOngoing software development
SIFTS - coordinating with other
biodatabases
CAPRI - Provide infrastructure for submission and maintenance of entries
PiMS
– Information management system for protein crystallography experimentsSlide55
PDBe Community Work
EuroCarbDBDatabases and bioinformatic tools in glycobiology and glycomics
BIObarA toolbar for browsing biological data and databases, a Mozilla plugin for your browserOutreach and training
Roadshows: invite us!TutorialsSlide56
PDBe Services: Future Emphasis
To go from being a historic structural archive to a valuable resource for structural biomedicinePDBeXploreProvide relevant interesting avenues to access structural informationLigands, Assemblies, Enzymes, GO, CATH, Sequences, Publications, Pathways
PDBe Validation ResourceProvide a comprehensive battery of validation tools during deposition and to the end-userMigrate and enhance EDS server
Partner with CCDC to bring cutting edge ligand validationSlide57
Summary
Structural Bioinformatics and Biocomputing are essential to fulfilling the promise of structural biologyDatabases are indispensible to all aspects of structural bioinformaticsPDB is the primary repository of structures and numerous databases are developed based on PDB.PDBe
provides high-quality services to depositors and end-users, and is an active member of structure-determination community.PDBe is open to all suggestions to make our services better and more relevant to your work.Slide58
Acknowledgements
Alejandro and organizers at IPMontPDBe groupSameer Velankar,
Jawahar SwaminathanDesigners, developers, maintainers of various structural databases at PDBe
and elsewhere