RCSB Protein Data BankAdvisory Committee

Teleconference Monday November 19, 2018

Meeting Participants§ AdvisoryCommittee• Participating:CynthiaWolberger(Chair),PaulAdams,PeterAndolfatto,JudyBlake,AndyByrd,BridgetCarragher,Wah Chiu,KirkClark,PaulCraig,RolandDunbrack,CathyPeishoff,SueRhee,Torsten Schwede,JillTrewhella

• Absent:RobertB.Darnell,PaulFalkowski,ThomasFerrin,AndrejSali*

§ RCSBPDB• Rutgers:StephenK.Burley,HelenM.Berman,JohnWestbrook,JasmineYoung,ChristineZardecki

• UCSD:ColeH.Christie

*Sali/UCSFwillformallyjoinRCSBPDBin2019 1

Highlights: 2017 - Present

13,049 structuresdeposited into the PDB

New structures added to the archive for a total of 136,472 entries

Over 1 million unique users served

>679 million data files downloaded from wwPDB

web and FTP sites

Annual IQB Boot Camp Single Particle Cryo-Electron Microscopy

Rutgers Undergraduate Course on Antimicrobial Resistance

wwPDB Summit

Molecule of the Month on Biodegradable

Plastic

wwPDB AC Meeting

RCSB PDB AC Meeting4th Annual Video Challenge Results Molecular View of Diabetes Treatment and Management

Year in the Life of the RCSB PDB Community

IQB Crash Course: Anti-cancer Immune

Checkpoint Therapies

3

Responses to 2017 RCSB PDB AC ReportCommitteestronglyencouragestheRCSBleadershiptousetherenewalasanopportunitytoexplainthesignificanceofeachactivityandhowasanintegratedwholetheyaddresstheneedsoftheresearch,industryandeducationcommunities.

Seriesofposters/flyersdocumentingRCSBPDBimpactandsupportforfederalfundingagencygoals

RCSBPDBimpactanalysespublishedinProteinScience,ScientificData

PDBImpactonRecentUSFDADrugApprovalsnowinpressatStructure

TheCommitteealsoencouragestheRCSBPDBtoaggressivelypursuenewsourcesofsupportbyapproachingprivatefoundations,pharmaceuticalcompaniesandNIHinstitutesthatutilizeRCSBPDBresourcesbutdonotcurrentlyprovidefunding.

Ongoing;Conversationsinitiatedwith• HHMI• NCI• SciencePhilanthropyAlliance• ScienceGatewaysCommunityInstitute

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RCSB PDB: Four Interoperating Services

CustomerServiceHelpDeskandITSupport

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Deposition/Biocuration

Archive Management/Access

1 2

DataExploration

3 4

Outreach/Education

• Deposition• Validation• Biocuration

• Datastandards• Dataintegration• Datastorage• Dataaccess

• Portal• Search• Browse• 3Dvisualization

• PDB-101

Deposition/Biocuration

Archive Management/Access1 2 Data

Exploration3 4 Outreach/Education

1. Deposition/Biocuration in 2017§ Ontrackfor~12,100depositionsin2018

§ 3DEMgrowthcontinuingin2018

Method 2017Depositions

2016Depositions

MX 11,889(91.2%)

10583

NMR 460(3.5%) 474

3DEM 658(5.0%) 531

Other 44(0.3%) 27

6

48%

31%

21%

2017ProcessingSites

PDBj

PDBe

RCSB PDB

30%

38%

21%

1%3% <1%

7%

2017DepositorLocationsNorth America

Europe

Asia

South America

Oceania

Africa

Commercial

1. Deposition/Biocuration in 2018§ OneDep• ORCiD nowmandatory• Biocuration moreefficient• SupportsSFX/XFELentries• Bettersoftwaremanagementvia GitHub

§ CarbohydrateRemediation• Collaborationwithglycoscience community

• Projectannounced atwwpdb.org

• PDBx/mmCIF Dictionaryextension and example filesavailable via GitHub

7

400450500550600650700750800

2009

2010

2011

2012

2013

2014

2015

2016

2017

#ofEntriesProcessed

Year

NewStructures/Biocurator

OneDep launched*

1. Deposition/Biocuration in 2019§ LigandValidationenhancement§ NMRRestraintValidationimplementation§ Author-initiatedCoordinatereplacement§ Carbohydrateremediation§ ChemicalComponentversioning§ OngoingDeposition/Biocuration efficiencyimprovement

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Master Copy ofPDB FTP

Repository

Depositors

DepositionBiocurationValidation

Archive keeping; Release coordination

Data Integration ServicesExchange DB

External Data Resources

OneDep

Archive Management/Access

Sequence &3D ClusteringServices

PDB Archive Data External Data

Sequence and 3D Data

RCSB PDB Copy of PDB

FTP Repository

GraphQL/REST APIs

ftp/RSYNCServices

Data Exploration

RCSB PDB Content Delivery Network

rcsb.org

Search Aggregator APIs

pdb101.rcsb.org

Data harvesting; Pre-deposition validation

Outreach/Education

Users

Programmers;External data resources

Researchers

Students; Teachers

Archive replicators; Power users; External data resources

Search Services

RCSB PDB Data Architecture Redesign

PDBx/mmCIF Data Schema Throughout!9

2. Archive Management/Access in 2018§ ExtendedPDBx/mmCIF dataschemaacrossallfourRCSBPDBservices

§ IntegratedArchiveManagement/AccessandDataExplorationbydevelopingnewAPIs(ApplicationProgramInterface)andWebServices

§ Legacysearchanddatadeliveryinfrastructurereplacedbycloudfriendlytechnologies(inbeta)• Searchindexingandsuggestions(ApacheSolr)• Archivingservices/updatestransitionedtoadistributedobjectstore(MongoDB)

• DataAccessservicestransitionedtoGraphQL API• Specializedsearch(Sequence&3D)featuresre-packagedasindependentWebServices

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2. Archive Management/Access in 2019§ UpgradeArchiveManagementdatastoragesystem§ ContinuetoproductionizenewservicearchitectureinsupportofthenewRCSB.org websitedesignandexpandedprogrammaticdataaccess

§ Continuetargetedremediation(carbohydrates)andextendeddataintegration(PubChem&CARD)

§ Continuecloudmigrationoftheweeklyupdateoperations

§ MigrateservicestoamoreportablepackagingusingDocker

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3. Data Exploration in 2017RCSB.org Users§ >395,000monthly,>1millionannually

§ 3%annualgrowthinnon-bounceuniqueusers

RCSB.org Sessions§ 35%growthsince2010§ Highaveragesessionduration(~6minutes)

§ Lowfractionof0-second“bounce”sessions

GlobalPDBDataDownloads§ Total:679,421,200total• FTP:454,723,083• Websites:224,698,117

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Potassium Channel (PDB 1bl8)Doyle et al. (1998) Science 280, 69-77

Frequently access structure––Structure data downloaded ~281K times since 2007

Cited >4700 times

3. Data Exploration in 2018§ Solr textsearchfunctionalityimplementedonRCSB.org (pilotedonPDB101.RCSB.org)

§ NewNGLvisualizationfeatures• Electrondensitymaps• Ligand-proteininteractions• Validationreportin3D

§ Newwebsitearchitecturedesigned/developed• Improvesspeedandscalingofexistingservices• Acceleratessoftwaredevelopmentofnewservices

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3. Data Exploration in 2019§ NewwebsitedesignutilizingAPIsfordeliveryofdatatoRCSB.org users

§ SameAPIssupportingprogrammaticaccesstoRCSB.org dataforpowerusers,externalresources

§ Newwebsitecapabilitiessupporting• Enhancedsearching(Solr plusotherdatatypes)• AutoSuggest,DrillDown,andAdvancedSearch• TabularReporting• BatchDataDownload

§ Mol*(mol-star)communitygraphicslibraryforincreasing/extendingNGLcapabilities

14

4. Outreach/Education in 2017/2018/2019§ >620KPDB-101Usersin2017

§ HealthFocus:Diabetes,AntibioticResistance• VideoChallenge• Curricularmaterials• GlobalHealthResources

15

What is an Enzyme?>142K views since 2017

>313K views since 2017

HPV

Any Questions About Recent Milestones?

16

wwPDB AC Meeting November 2, 2018§ IntroducedChair-Elect(PeterRosenthal,UK)

§ Reviewed2017metrics

§ Reviewed2017/2018progressversus goals

§ DescribednewwwPDBorganizationalstructure

§ ExplainednewfeaturesofrevisedwwPDBCharter(totakeeffectJanuary1st 2019)

§ Outlined2018/2019goals

§ Obtainedconcurrenceonvariouspolicymatters

§ ThankedoutgoingChair(AndyByrd,US)

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New wwPDB Organizational Structure

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CORE ARCHIVES

PDBBMRBEMDB

EMPIAR

SASBDB

MX Images

CORE MEMBERSRCSB PDB

PDBePDBj

BMRB EMDB

FEDERATED RESOURCES

wwPDB Core Archives

Definition:AwwPDB“CoreArchive”isaglobalstructuralbiologydataresourcejointlymanagedbywwPDBCoreMembers.

§ CurrentwwPDBCoreArchives:• PDBCoreArchive:3DStructureDataResourcehousingmultiscale/atomicstructuralmodelsplusmoleculardataandmetadata,MXexperimentaldataandmetadata,andotherexperimentaldata.(ArchiveKeeper:RCSBPDB)

• BMRBCoreArchive:BiomolecularNMRDataResource housingmoleculardataandmetadata,NMRexperimentaldataandmetadata,andotherexperimentaldata.(ArchiveKeeper:BMRB)

§ NextCoreArchiveexpectedtojoinwwPDB:• EMDBCoreArchive:MolecularandCellularEMDataResource housingmolecular/biologicaldataandmetadata,experimentalelectricpotentialmapdata,andotherexperimentaldata.(ArchiveKeeper:EMDB) 19

Any Questions About wwPDB AC?

20

Discussion Topics

21

Urgent Matters§ Fundraising:Othersuggestions?

§ MembershipTransitions• Chair:2019- 2021• NSFReviewPanelsuggestedinclusionofadditionaldimensionsofdiversity,especially...membersfromunderrepresentedcommunities,andexperienceindiverseorganizationtypes

§ RCSBPDBACMeetingschedule2019andbeyond

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Membership Transitions§ NewChair:PaulD.Adams• DivisionDirectorMolecularBiophysics&IntegratedBioimagingLawrenceBerkeleyNationalLaboratory

§ NewMember:Mandë Holford• AssociateProfessorDepartmentofChemistry andBiochemistryHunterCollegeBelfer ResearchBuildingandCUNYGraduateCenter

• ResearchAssociateSacklerInstitutefor ComparativeGenomicsInvertebrateZoologyAmericanMuseumof NaturalHistory

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RCSB PDB AC Meeting Schedule

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§ OurFallMeetingsconflictwithwwPDBAC

§ Proposedmeetingplanfor2019-2023• Spring2019• TargetWindowMondayApril1- ThursdayApril4

• Spring2020• PDB50in2021• RepeatWashington,DCareameetingtoenableprogramofficerparticipationinSpring2022

Planning ongoing for PDB 2021

25October 20, 1971Nature New Biology

Many Thanks to the RCSB PDB AC§ Commentsontherenewalproposalweremuchappreciated

§ FeedbackonourMay2018SiteVisitpresentationsalsoprovidedsignificantbenefit

§ Lookforwardtoyourongoingfeedbackon• New2019RCSB.org websitedesign• SFX/XFEL• 3DEM(single-particleandtomography)• Integrative/HybridMethods

§ Yourhelpwithfundraisingactivitiesgoingforward

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Many Thanks to Cynthia Wolbergerfor 10 Years of Advice and Support

27

RCSB PDB AC member since 2009 RCSB PDB Chair, 2013-2018

Celebration of Open Access in Structural Biology Symposium, 2013

RCSB PDB AC 2010

Join the RCSB Protein Data Bank at University of California San Diego

Open Positions:

Postdoctoral Fellows

The Challenge:Develop innovative analysis, integration, query, and visualization tools for 3D biomolecular structures to help accelerate research and training in biology, medicine, and related disciplines.

RCSB PDB Team

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RCSB PDB is funded by a grant (DBI-1338415) from the National Science Foundation, the National Cancer Institute, the National Institute of General Medical Sciences, and the US Department of Energy

RCSB PDB is a member of the Worldwide Protein Data Bank partnership (wwPDB; wwpdb.org)

RCSB.ORGinfo@rcsb.org

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