Poster: Scalable 3D molecular graphics on the web @ 3Dsig and Web3D 2016

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Scalable3DmoleculargraphicsonthewebPDB a billion atom archiveSteps 1 + 2: Speeding-up download & parsingFunding and acknowledgementsStep 4: Molecular representations geometryStep 3: Efficient storage & accessSteps to display a structureGrowth of the PDB archiveStep 5: Rendering without pluginsDoes it scale?>1BillionatomsintheasymmetricunitsInstancing:Creategeometryonce,sendtoGPUonce,thentransformposition&rendermultipletimes. Greensurfaceisreused59timesforhighlysymmetricviruscapsidImpostors:ForeachpixelGPUtestsintersectionofsphereandcameraraytoreducetrianglecount. Qualityresolutionindependentasmorepixelsaretested Impostorsalsousedforcylinders. JavaAppletshaveprovidedfastexecutionandGPUaccess RemovedfromGoogleChromeinversion45(Sep2015) OracletodeprecateJavaplugininupcomingJDK9 Browsersdontneedpluginsanymore JavaScriptapproachesnativespeed WebGLoffersplugin-freeaccesstothegraphicscardHIV-1capsidatthreescales:216hexamericand 12pentamericsubunits,~2.4MuniqueatomsFaustovirusmajorcapsid:2760instancesof14478uniqueatoms,~40MoverallatomsAlexanderS.Rose,AnthonyR.Bradley,YanaValasatava,JoseM.Duarte,AndreasPrli,PeterW.Rose Largeststructure:HIV-1Capsid(PDBID3J3Q) ~2.4Muniqueatoms gzippedmmCIFfile:48.7MB 68ofthe100largeststructuresdepositedinpast3years AdvancesinexperimentaltechniquesfuelthegrowthDownloadFileDecompress&ParsePopulateDataModelCreateGeometryRenderBD2K Grant: U01 CA198942 RCSB PDB Team MMTF Libraries&Specification:http://mmtf.rcsb.org NGLViewer SupportsMMTF,usescolumnarstores&WebGL Openlydeveloped:https://github.com/arose/nglASRose&PWHildebrand.NGLViewer:awebapplicationformolecularvisualization.Nucl.AcidsRes.(1July2015)43(W1).doi:10.1093/nar/gkv402 ThePDBarchiveisgrowing:structuresaregettinglargerandmorecomplex Herewepresentapproachesforscalable3Dmoleculargraphicsontheweb TheMMTFformatprovideshighlycompressedstructurefiles TheNGLViewerefficientlystores&rendersmillionsofatoms Eventhelargeststructurescanberapidlydownloaded&displayedinabout1secondto1minutedependingondeviceandconnectionspeedNGLViewer MacroMolecularTransmissionFormat(MMTF) Newfileformat,optimizedfortransmissionofmacromolecules Binary-forfastparsing MessagePackbinaryJSON"asanextensiblecontainer Bespokecompressionstrategies-forsmallfilesize ComparisonwithmmCIF(wholePDBarchive,gzipped) Sizereducedbyafactorof>4(30GBto7GB) Parsingtimereducedbyafactorof~12(205minto17min) usingJavaScriptlibrariesMMTF Columnarstores SingleTypedArrayperproperty Parseddatacanbecopiedinblocks ConvenientaccessviaproxyobjectsSoftware availabilityPDBID1RB8PDBID3J3QPDBID5J7VImpostorGeometry2TrianglesNormalGeometry320Triangles1. 2. 3. 4. 5. http://mmtf.rcsb.orghttps://github.com/arose/ngl