EMBL-EBI Annual Scientific Report 2012

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PDBe content and integrationOur goal is to ensure that PDBe truly serves the needs of the biomedicalcommunity. We are constantly improving PDBe’s web interface anddesigning new tools to make structural data available toall.In the context of the SIFTS project, we integrate structural data with other biological data to facilitate discovery. Theseintegrated data form the basis for many query interfaces that allow biomacromolecular structure data to be presented inits biological context. Our specific focus areas are: data integrity, data quality, integration and data dissemination to thenon-expert biomedical community.Major achievementsIn 2012 PDBe annotation staff curated a record number ofPDB entries (1676 entries, up 12% from 2011), the majorityof which were annotated within one working day of being deposited.PDBe staff also annotated 253 EMDB entries - 58%of all EMDB entries deposited in 2012. One of these entrieswas the 1000th EMDB entry to be processed at EMBL-EBIsince the EMDB archive was established here in 2002.PDBe staff, in collaboration with other wwPDB members,carried out a remediation project to improve therepresentation of the biologically important peptide-likeantibiotic and inhibitor molecules in the PDB. The remediationefforts addressed issues related to consistent representationand functional annotation of these molecules. A collectionof almost 600 reference dictionary files, containing detailedchemical and functional description of antibiotic and inhibitormolecules, was made available through the PDB ftp area.We remediated EMDB data to improve the quality andconsistency of the archive. Our team addressed issues relatedto taxonomy information, author and citation information,map-symmetry records and consistent representation of allEMDB map files.Validation information about newly deposited structures (aswell as those already in the public archive) is a critical elementof usability. PDBe implemented an initial version of thevalidation-software pipeline as part of the new Deposition andAnnotation system, developed in collaboration with the otherwwPDB partners.Since 2000, PDBe has provided valuable integration servicesvia SIFTS (Structure Integration with Function, Taxonomyand Sequences), which is maintained in close collaborationwith the UniProt team. SIFTS supports several PDBe toolsand services and is used by many other major bioinformaticsresources. We improved the SIFTS infrastructure and thecoverage of mapping information, upgrading the versioningand adding new data on GO and InterPro assignments.Our team undertook the redesign of the PDBe website andsearch infrastructure, which is scheduled to launch in 2013.We worked with many users in both academic and industrysectors to better understand how they use and navigatestructure-related information; our findings formed the basis ofthe redesign. We are also revamping the search infrastructurefor PDB and EMDB data and developing an API for accessingstructure data.Future plansWe strive to make biomacromolecular structure data availablein useful ways to a broad biomedical community. Wecontinually improve the quality and integrity of the data in ourcare, and endeavor to integrate them with other sources ofbiomedical information.We will work with our wwPDB partners to simplify thequality assessment of crystal structure entries in the PDBby progressing an X-ray validation pipeline, which wasdeveloped at PDBe. We will also develop similar pipelinesfor NMR and 3DEM data, again making quality assessmenteasier for non-expert users. We will design a more intuitiveinterface to display validation information for all kinds of3D biomacromolecular structure data, and will launch acompletely redesigned web site in 2013.A new wwPDB Deposition and Annotation system will bereleased in 2013, and we expect this to result in a majorchange in annotation practices. We will work closely with theother wwPDB partners to ensure an efficient transition.40 2012 EMBL-EBI Annual Scientific Report
Sameer VelankarPhD, Indian Institute of Science, 1997. Postdoctoralresearcher, Oxford University, UK,1997-2000.At EMBL-EBI since 2000. Team leadersince 2011.Figure. The wwPDB X-ray validation pipeline assesses the quality of experimental data, the atomic model and the fit of the model to the data,using community-standard software. The pipeline will be run for all structures already in the PDB archive and also for all newly depositedstructures. It produces high-quality statistics, graphs, plots and a summary report to help expert and non-expert users assess the global andlocal quality of individual PDB entries so they can decide if it is suitable for their needs. The validation results can be used to compare andselect the most suitable model of a particular biomacromolecule in the entire PDB.Selected referencesVelankar, S., et al. (2012) PDBe: Protein Data Bank in Europe.Nucleic Acids Res 40, D445-D452.Gore, S., Velankar, S. and Kleywegt, G.J. (2012) Implementingan X-ray validation pipeline for the Protein Data Bank. ActaCrystallogr D68, 478-483.2012 EMBL-EBI Annual Scientific Report41
Page 1 and 2: EMBL-European Bioinformatics Instit
Page 3: Table of contentsIntroduction & ove
Page 6 and 7: EMBL-EBI 2012It was a year of trans
Page 8 and 9: New service developments• Underst
Page 10 and 11: Organisation ofEMBL-EBI Leadership
Page 12 and 13: dGenes, genomes and variationThe Eu
Page 14 and 15: dGenes, genomes and variationSummar
Page 16 and 17: European Nucleotide ArchiveOur team
Page 18 and 19: Vertebrate genomicsThe Vertebrate G
Page 20 and 21: Nonvertebrate genomicsWe provide to
Page 22 and 23: gMolecular atlasLife scientists are
Page 24 and 25: Functional genomicsThe Functional G
Page 26 and 27: Functional genomics productionOur t
Page 28 and 29: Functional genomics developmentOur
Page 30 and 31: PProteins and protein familiesUniPr
Page 32 and 33: UniProt contentOne of the central a
Page 34 and 35: UniProt developmentOur team provide
Page 36 and 37: InterProOur team co-ordinates the I
Page 38 and 39: sMolecular and cellular structureUn
Page 40 and 41: Protein Data Bank in EuropeThe majo
Page 44 and 45: PDBe databases and servicesOur team
Page 46 and 47: yMolecular systemsThe genes and gen
Page 48 and 49: Proteomics servicesThe Proteomics S
Page 50 and 51: Chemical biologyThe importance of s
Page 52 and 53: ChEMBLThe ChEMBL team develops and
Page 54 and 55: Cheminformatics and metabolismOur t
Page 56 and 57: cCross-domain toolsand resourcesSci
Page 58 and 59: Literature servicesScientific liter
Page 60 and 61: Research2012 has seen the further t
Page 62 and 63: Bertone groupPluripotency, reprogra
Page 64 and 65: Birney groupNucleotide dataDNA sequ
Page 66 and 67: Enright groupFunctional genomics an
Page 68 and 69: Goldman groupEvolutionary tools for
Page 70 and 71: Le Novère groupComputational syste
Page 72 and 73: Luscombe groupGenomics and regulato
Page 74 and 75: Marioni groupComputational and evol
Page 76 and 77: Rebholz groupPhenotypes and multili
Page 78 and 79: Saez-Rodriguez groupSystems biomedi
Page 80 and 81: Thornton groupProteins: structure,
Page 82 and 83: The EMBL International PhDProgramme
Page 84 and 85: SupportOur support teams provide fo
Page 86 and 87: T TrainingAs part of EMBL-EBI’s m
Page 88 and 89: IIndustry programmeSince 1996 the I
Page 90 and 91: NExternal relationsAs a European In
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sExternal servicesOur team manages
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SSystems and networkingOur team man
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q AdministrationThe EMBL-EBI Admini
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Funding and resource allocationDesp
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Growth of core resourcesIn 2012 the
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CollaborationsEMBL-EBI is a highly
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Staff growthOur organisational stru
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Scientific advisory commiteesEMBL S
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The International Nucleotide Sequen
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EMDataBank Advisory Committee• Jo
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Major database collaborationsARRAYE
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THE GENE ONTOLOGY CONSORTIUM• Agb
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REACTOME• New York University Med
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Publications in 2012In 2012, EMBL-E
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Doreleijers, J. F., Vranken W. F.,
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Kruger, F. A., Rostom R. and Overin
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Sahakyan, Aleksandr B., Cavalli And
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EMBL - European Bioinformatics Inst
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EMBL-EBI Annual Scientific Report 2012

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