Structure Databases: - PowerPoint Presentation

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