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

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Molecular Biology Toolkit (MBT)http//mbt.sdsc.ed
u

• A Java toolkit for molecular visualization

John Moreland Apostol Gramda PI Phil Bourne
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What is MBT?

• Java toolkit for developing custom molecular
  visualization applications
• High-qualityinteractive3D rendering
• and more

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MBT Functionality

• Provides
• Data loading
• Local files (PDB, mmCIF, Fasta, etc)
• Compressed files (zip, gzip)
• Remote (http, ftp, database, etc)
• Efficient data access
• Raw data (Structure)
• Derived data (StructureMap)
• Vizualization (plug-in Viewers)

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MBT Architecture
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Loading data

• Local PDB file
• Structure structure StructureFactory.load( new
  File( data/1STN.pdb ) )
• Remote compressed mmCIF URL
• Structure structure StructureFactory.load( new
  URL( http//mbt.sdsc.edu/data/5ebx.cif.gz ) )
• PDB ID Code
• Structure structure StructureFactory.load(
  4hhb )

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Accessing raw data

• The Structure Class
• int atomCount structure.getStructureComponentCou
  nt(
• SturctureComponentRegistry.TYPE_ATOM )
• for ( int i0 iltatomCount i )
• Atom atom structure.getStructureComponentByInde
  x(
• SturctureComponentRegistry.TYPE_ATOM, i )
• System.out.println( atom.coordinate0 )

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Accessing derived data

• The StructureMap Class
• Primary Structure
• Atom -gt Residue -gt Chain -gt etc
• Secondary Structure
• From source data (conformations)
• Computed (eg Kabsh Sander)
• Bonds

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MBT StructureDocument

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

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MBT Viewers

• StructureViewer
• 3D primary and secondary structure display
• Sequence Viewer
• Residue display
• TreeViewer
• Hierarchical display
• Others (MultSeq)

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StructureViewer

• Primary Structure
• Balls Sticks, CPK spheres, Bonds
• Secondary Structure
• Helix, Turn, Strand, Coil
• Backbone traces

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3D Geometry Engine

• General / Re-usable components
• Extrusion class supporting arbitrary
  cross-sections with twist and scale along
  path
• Cached/shared sphere geometry
• Cached/shared color attributes
• Consistent shape interconnections
• Path continuity
• Smooth shape-to-shape transitions

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Optimized for Large Molecules

• Loaders optimized for speed and small memory
  footprint
• List and hierarchical data views
• Sorts data where possible for O(logN) binary
  searches
• Display styles use RangeMaps to coalesce
  attribute references
• Style interfaces reduce storage of duplicate
  scalar values

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MBT Demos

• Local 4hhb PDB
• Remote 10mh Gzip mmCIF
• Examples
• Filters
• StructureMapping
• Styles

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MBT Status

• Now Supports
• Derived Secondary Structures
• Ligand map display
• Working on
• Style and authoring classes
• Contributors
• Multiple Sequence Alignment viewer (PKR)
• Kinase Database Loader (PKR)
• Rasmol/Chime Scripting Engine (RIT)

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MBT Futures

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

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MBT Team

• Philip E. Bourne, PhD (UCSD)
• Project principle investigator
• Apostol Gramada (UCSD)
• Postdoc, toolkit co-developer
• John L. Moreland (SDSC)
• Project technical lead, toolkit co-developer

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MBT Collaborators

• Sasha Buzko (UCSD)
• GUIs, Authoring, Data Structures
• Paul Craig, PhD (RIT)
• Biochemistry consulting, Scripting
• Douglas S. Greer, PhD (UCSD)
• Software design, OpenMMS toolkit
• John Tate, PhD (UCSD)
• MBT prototype co-designer
• And many more!

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MBT Fundiing

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

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Questions?

• For more information, visit
• http//mbt.sdsc.edu

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Sizes (bytes)

• Application
• 5,460 SimpleViewer_signed.jar
• Toolkit
• 487,208 mbt_0.0.4_bin_signed.jar
• Java/Java3D (one time)
• 10,244,264 JRE 1.4.1_02
• 2,703,177 Java3D 1.2.1_04

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MBT Overview

• A Java molecular visualization toolkit
• Local file remotedata loaders for PDB,mmCIF,
  Fasta,
• Coupled 2D/3D views
• Rich extensible API
• Portable web-deployable Java