EuroVis 2005 1Computer Graphics, TU Braunschweig

“BioBrowser: A Framework for Fast Protein Visualization”

Andreas Halm, Lars Offen, Dieter Fellner (TU Braunschweig)

IEEE VGTC Symposium on Visualization (2005)

EuroVis 2005 2Computer Graphics, TU Braunschweig

Overview

Existing tools Motivation BioBrowser

Overall concepts Different visualization styles

Future work Live Demo

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Existing Tools Visualization Tools

RasMol, Chimera, PyMol, Yasara, and others Modeling Tools

VMD (Visual Molecular Dynamics), NAMD (Scalable Molecular Dynamics), ProtoShop (Interactive Protein Manipulation), etc.

Database Tools BLAST, FASTA (search for similar structures)

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Motivation

Increasing number of structurally fully analyzed molecules

Many different sources of information, e.g. Protein database UniProt GenomeNet

Provide a tool, which integrates this information into the 3D structure of the molecule … (where it really belongs)

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BioBrowser - Goals

Provide an integrated access and visualization tool for existing information sources

Challenges: Visualization (make access as smooth as possible)

Support all common visualization styles Interactive presentation of huge datasets Keep precomputed data to a minimum

Integration of the information Interaction with existing tools for data collection Integrate collected information into 3D space

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Overall Concepts I Visualization of huge data sets in real time

Just-in-Time generation of the geometry Reduction of geometry through

Level-of-Detail Billboarding Subdivision-Approaches

Use of modern GPU Features Minimizing precomputed vis-related data

Designing/Use of fast algorithms Data (e.g. solvent surface geometry) can be made

available in real time

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Overall Concepts II

Ensure Extensibility Compact Interface for plugins to integrate new

modules (which also supports) Communication between the different modules

Platform independent No usage of platform-dependent libraries, like

MFC Use of wxWidgets Version for: Windows, Linux, Cave, Mozilla/IE-

Plugin, PDA (work in progress)

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Visualization Styles

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Different approachesD

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LOD-Meshes

Modeled polytopesSubdivision Surfaces

Adding depth Texture =>Depth sprites

Fully GPU rendered

Ray-shooting on the GPU[Klein&Ertl 2004]

Billboards

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Ball and Stick Spheres don’t intersect and

the bonds intersect them in a predictable manner=> use billboards,

results in four verticesper billboard

If graphics board is capable of vertex/fragment shaders use a ray-shooting shader => only one vertex per

atom or bond

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Spacefill

Using van der Waals radius for atoms

Different approaches (GPU capability)

LOD-Meshes Depth sprites Fully GPU rendered

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Ribbons

Represents the structure of the backbone

Cα-atoms used for

position and appearance

Three different kinds: Helices, -Strands,

turns

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Ribbons – Technique

Coarse base mesh Build quads

Subdivision usingcombined BReps (polygonal faces + Catmull/Clark)

Fine tuning of subdivision level

Curvature, projected size, idle time

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Surfaces

What are molecular surfaces?

Instead of using fixed resolution (like Marching Cubes), use subdivision surfaces

Leads to both: high quality

visualization interactivity

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Surfaces – Calculation

Calculation: Molecule Spacefill Reduced

Surfaces Base mesh Subdivision

surfaces

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Structural Lens

Combine different visualization styles using their respective technique

Improve understanding which substructures define the surface and, therefore, determine the molecule’s function

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Future Work

Integrate common tools (e.g. as plug-ins) Sequence-analysis/alignment

Blast FASTA

Structure definition DSSP

Embed additional bio-information, collected from internet or local databases into 3D-structure

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Credit

The BioBrowser results from a collaboration project (funded by the German Research Foundation, DFG) between the

Institute of Computer Graphics, TU Braunschweig and

Structural Biology,Ges. f. Biotechnologische Forschung (GBF), D. Heinz, G. Dieterich, J. Reichelt

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Live Demo

Demo

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Thank you for your attention!