molecular biology toolkit (mbt) mbt.sdsc

Molecular Biology Toolkit Molecular Biology Toolkit (MBT)(MBT)http://mbt.sdsc.eduhttp://mbt.sdsc.edu

A Java toolkit for A Java toolkit for molecular visualizationmolecular visualization

John MorelandJohn MorelandApostol GramdaApostol GramdaPI: Phil BournePI: Phil Bourne

SAN DIEGO SUPERCOMPUTER CENTER

University of California, San Diego SDSCSDSC

What is MBT?What is MBT?

• Java toolkit for developing custom Java toolkit for developing custom molecular visualization applicationsmolecular visualization applications

• High-qualityHigh-qualityinteractiveinteractive3D rendering3D rendering

• and more…and more…



MBT FunctionalityMBT Functionality

• ProvidesProvides– Data loadingData loading

• Local files (PDB, mmCIF, Fasta, etc)Local files (PDB, mmCIF, Fasta, etc)• Compressed files (zip, gzip)Compressed files (zip, gzip)• Remote (http, ftp, database, etc)Remote (http, ftp, database, etc)

– Efficient data accessEfficient data access• Raw data (Structure)Raw data (Structure)• Derived data (StructureMap)Derived data (StructureMap)

– Vizualization (plug-in Viewers)Vizualization (plug-in Viewers)



MBT ArchitectureMBT Architecture



Loading dataLoading data

• Local PDB fileLocal PDB fileStructure structure = StructureFactory.load(Structure structure = StructureFactory.load(

new File( “data/1STN.pdb” ) );new File( “data/1STN.pdb” ) );

• Remote compressed mmCIF URLRemote compressed mmCIF URLStructure structure = StructureFactory.load(Structure structure = StructureFactory.load(

new URL( “http://mbt.sdsc.edu/data/5ebx.cif.gz” new URL( “http://mbt.sdsc.edu/data/5ebx.cif.gz” ) );) );

• PDB ID CodePDB ID CodeStructure structure = StructureFactory.load( “4hhb” );Structure structure = StructureFactory.load( “4hhb” );



Accessing raw dataAccessing raw data

• The Structure ClassThe Structure Classint atomCount = structure.getStructureComponentCount(int atomCount = structure.getStructureComponentCount(

SturctureComponentRegistry.TYPE_ATOM );SturctureComponentRegistry.TYPE_ATOM );

for ( int i=0; i<atomCount; i++ )for ( int i=0; i<atomCount; i++ )

{{

Atom atom = structure.getStructureComponentByIndex(Atom atom = structure.getStructureComponentByIndex(

SturctureComponentRegistry.TYPE_ATOM, SturctureComponentRegistry.TYPE_ATOM, i );i );

System.out.println( atom.coordinate[0] );System.out.println( atom.coordinate[0] );

}}



Accessing derived dataAccessing derived data

• The StructureMap ClassThe StructureMap Class– Primary StructurePrimary Structure

• Atom -> Residue -> Chain -> etc…Atom -> Residue -> Chain -> etc…

– Secondary StructureSecondary Structure• From source data (conformations)From source data (conformations)• Computed (eg: Kabsh & Sander)Computed (eg: Kabsh & Sander)

– BondsBonds



MBT StructureDocumentMBT StructureDocument

• A StructureDocument contains A StructureDocument contains Structures and provides event Structures and provides event propagation to all Viewerspropagation to all Viewers

• Viewers view Viewers view StructureDocument contentStructureDocument content



MBT ViewersMBT Viewers

• StructureViewerStructureViewer– 3D primary and secondary structure 3D primary and secondary structure

displaydisplay• Sequence ViewerSequence Viewer

– Residue displayResidue display• TreeViewerTreeViewer

– Hierarchical displayHierarchical display• Others (MultSeq)Others (MultSeq)



StructureViewerStructureViewer

• Primary StructurePrimary Structure– Balls & Sticks, CPK spheres, BondsBalls & Sticks, CPK spheres, Bonds

• Secondary StructureSecondary Structure– Helix, Turn, Strand, CoilHelix, Turn, Strand, Coil

• Backbone tracesBackbone traces



3D Geometry Engine3D Geometry Engine

• General / Re-usable componentsGeneral / Re-usable components– Extrusion class supporting arbitrary cross-Extrusion class supporting arbitrary cross-

sections with “twist” and “scale” along pathsections with “twist” and “scale” along path– Cached/shared sphere geometryCached/shared sphere geometry– Cached/shared color attributesCached/shared color attributes

• Consistent shape interconnectionsConsistent shape interconnections– Path continuityPath continuity– Smooth shape-to-shape transitionsSmooth shape-to-shape transitions



Optimized for Large Optimized for Large MoleculesMolecules

• Loaders optimized for speed and small Loaders optimized for speed and small memory footprintmemory footprint

• List and hierarchical data viewsList and hierarchical data views• Sorts data where possible for O(logN) Sorts data where possible for O(logN)

binary searchesbinary searches• Display styles use “RangeMaps” to Display styles use “RangeMaps” to

coalesce attribute referencescoalesce attribute references• Style “interfaces” reduce storage of Style “interfaces” reduce storage of

duplicate scalar valuesduplicate scalar values



MBT DemosMBT Demos

• Local 4hhb PDBLocal 4hhb PDB• Remote 10mh Gzip mmCIFRemote 10mh Gzip mmCIF• ExamplesExamples

– FiltersFilters– StructureMappingStructureMapping– StylesStyles



MBT StatusMBT Status

• Now SupportsNow Supports– Derived Secondary StructuresDerived Secondary Structures– Ligand map & displayLigand map & display

• Working onWorking on– Style and authoring classesStyle and authoring classes

• ContributorsContributors– Multiple Sequence Alignment viewer (PKR)Multiple Sequence Alignment viewer (PKR)– Kinase Database Loader (PKR)Kinase Database Loader (PKR)– Rasmol/Chime Scripting Engine (RIT)Rasmol/Chime Scripting Engine (RIT)



MBT FuturesMBT Futures

• RNA/DNA chain “cartoons”RNA/DNA chain “cartoons”• Surfaces (computed, imported)Surfaces (computed, imported)• LOTS of GUI classesLOTS of GUI classes• XML import/export (Data and XML import/export (Data and

Authored Documents)Authored Documents)



MBT TeamMBT Team

Philip E. Bourne, PhD (UCSD)Philip E. Bourne, PhD (UCSD)Project principle investigatorProject principle investigator

Apostol Gramada (UCSD)Apostol Gramada (UCSD)Postdoc, toolkit co-developerPostdoc, toolkit co-developer

John L. Moreland (SDSC)John L. Moreland (SDSC)Project technical lead, toolkit co-Project technical lead, toolkit co-

developerdeveloper



MBT CollaboratorsMBT Collaborators

• Sasha Buzko (UCSD)Sasha Buzko (UCSD)– GUIs, Authoring, Data Structures GUIs, Authoring, Data Structures

• Paul Craig, PhD (RIT)Paul Craig, PhD (RIT)– Biochemistry consulting, ScriptingBiochemistry consulting, Scripting

• Douglas S. Greer, PhD (UCSD)Douglas S. Greer, PhD (UCSD)– Software design, OpenMMS toolkitSoftware design, OpenMMS toolkit

• John Tate, PhD (UCSD)John Tate, PhD (UCSD)– MBT prototype co-designerMBT prototype co-designer

• And many more!And many more!



MBT FundiingMBT Fundiing

• This project was funded as part of This project was funded as part of the NIH PPG grant number 1-P01-the NIH PPG grant number 1-P01-GM63208 and its NIGMS division.GM63208 and its NIGMS division.



Questions?Questions?

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http://http://mbtmbt..sdscsdsc..eduedu