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

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  • Scalable3Dmoleculargraphicsontheweb

    PDB a billion atom archive

    Steps 1 + 2: Speeding-up download & parsing

    Funding and acknowledgements

    Step 4: Molecular representations geometry

    Step 3: Efficient storage & access

    Steps to display a structure

    Growth of the PDB archive

    Step 5: Rendering without plugins

    Does it scale?

    >1Billionatomsintheasymmetricunits

    Instancing:Creategeometryonce,sendtoGPUonce,thentransformposition&rendermultipletimes.

    Greensurfaceisreused59timesforhighlysymmetricviruscapsid

    Impostors:ForeachpixelGPUtestsintersectionofsphereandcameraraytoreducetrianglecount.

    Qualityresolutionindependentasmorepixelsaretested

    Impostorsalsousedforcylinders.

    JavaAppletshaveprovidedfastexecutionandGPUaccess RemovedfromGoogleChromeinversion45(Sep2015) OracletodeprecateJavaplugininupcomingJDK9

    Browsersdontneedpluginsanymore JavaScriptapproachesnativespeed WebGLoffersplugin-freeaccesstothegraphicscard

    HIV-1capsidatthreescales:216hexamericand 12pentamericsubunits,~2.4Muniqueatoms

    Faustovirusmajorcapsid:2760instancesof14478uniqueatoms,~40Moverallatoms

    AlexanderS.Rose,AnthonyR.Bradley,YanaValasatava,JoseM.Duarte,AndreasPrli,PeterW.Rose

    Largeststructure:HIV-1Capsid(PDBID3J3Q) ~2.4Muniqueatoms gzippedmmCIFfile:48.7MB

    68ofthe100largeststructuresdepositedinpast3years Advancesinexperimentaltechniquesfuelthegrowth

    DownloadFileDecompress&ParsePopulateDataModelCreateGeometryRender

    BD2K Grant: U01 CA198942 RCSB PDB Team

    MMTF Libraries&Specification:http://mmtf.rcsb.org

    NGLViewer SupportsMMTF,usescolumnarstores&WebGL Openlydeveloped:https://github.com/arose/ngl

    ASRose&PWHildebrand.NGLViewer:awebapplicationformolecularvisualization.Nucl.AcidsRes.(1July2015)43(W1).doi:10.1093/nar/gkv402

    ThePDBarchiveisgrowing:structuresaregettinglargerandmorecomplex Herewepresentapproachesforscalable3Dmoleculargraphicsontheweb

    TheMMTFformatprovideshighlycompressedstructurefiles TheNGLViewerefficientlystores&rendersmillionsofatoms

    Eventhelargeststructurescanberapidlydownloaded&displayedinabout1secondto1minutedependingondeviceandconnectionspeed

    NGLViewer

    MacroMolecularTransmissionFormat(MMTF) Newfileformat,optimizedfortransmissionofmacromolecules Binary-forfastparsing

    MessagePackbinaryJSON"asanextensiblecontainer Bespokecompressionstrategies-forsmallfilesize

    ComparisonwithmmCIF(wholePDBarchive,gzipped) Sizereducedbyafactorof>4(30GBto7GB) Parsingtimereducedbyafactorof~12(205minto17min) usingJavaScriptlibraries

    MMTF

    Columnarstores SingleTypedArrayperproperty Parseddatacanbecopiedinblocks Convenientaccessviaproxyobjects

    Software availability

    PDBID1RB8

    PDBID3J3Q

    PDBID5J7V

    ImpostorGeometry2Triangles

    NormalGeometry320Triangles

    1. 2. 3. 4. 5.

    http://mmtf.rcsb.orghttps://github.com/arose/ngl

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