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

• Browsersdon’tneedpluginsanymore• JavaScriptapproachesnativespeed• WebGLoffersplugin-freeaccesstothegraphicscard

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

Faustovirusmajorcapsid:2760instancesof14478uniqueatoms,~40Moverallatoms

AlexanderS.Rose,AnthonyR.Bradley,YanaValasatava,JoseM.Duarte,AndreasPrlić,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• MessagePack“binaryJSON"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.