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Miklós Vargyas, Judit Papp
May, 2005
MarvinSpace – live demo
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Slide 2
MarvinSpace — UGM 2005
Description of MarvinSpace
• high performance 3D molecule visualization tool
• WEB enabled, platform independent
• available as • standalone application with an easy-to-use GUI• Java Applet • developers' toolkit
• visualizes
• small molecules, proteins, nucleic acids, crystals,
• molecular surfaces, molecular orbitals, volumetric data
• methods for
• molecular overlay,
• geometry optimization and conformer generation
• share molecular information by labeling and annotating atoms, bonds, ligands, receptors, complexes, surface regions
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Slide 3
MarvinSpace — UGM 2005
Features of MarvinSpace
Key features of v1.0
• pure java (all platforms, html integration)
• programmable (via java API)
• extendable (custom components, calculations (e.g. property grids for surface coloring) can be integrated)
• professional support (24 hour response time, rapid implementation of feature requests etc)
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Slide 4
MarvinSpace — UGM 2005
Features of MarvinSpace
Other features of v1.0
• table view (multiple cells)
• multiple molecule view (docked ligands; show/hide, load/remove)
• ball, stick, spacefill, cartoon representation
• various surface calculations: molecular, solvent accessible, Connolly; blobby
• property mapping on surface (e.g. electrostatic potential), dynamic surface coloring, transparency
• distance and angle measurement; change of conformation about rotatable bonds
• high quality rendering (depth cueing, perspective projection, antialiasing)
• dynamic scaling of rendering quality based on actual frame rate
• clipping
• atom, bond, residue, molecule, surface component picking
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Slide 5
MarvinSpace — UGM 2005
Examples of MarvinSpace
• atoms are spheres, not ragged polyhedra.
• Proper lights and reflections, not a uniform lit ball placed at every atom position.
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Slide 6
MarvinSpace — UGM 2005
Examples of MarvinSpace
• Optional depth cueing (fog effect)
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Slide 7
MarvinSpace — UGM 2005
Examples of MarvinSpace
• smooth surfaces
• no missing or odd triangles
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Slide 8
MarvinSpace — UGM 2005
Examples of MarvinSpace
• fast, novel algorithm, not the common analytic approach
• accurate saddle for three and more nearby atoms
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Slide 9
MarvinSpace — UGM 2005
Examples of MarvinSpace
• Blobby molecule: a novel approach to surface representation
• easy to configure to obtain smooth surfaces
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Slide 10
MarvinSpace — UGM 2005
Examples of MarvinSpace
• antialiasing
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Slide 11
MarvinSpace — UGM 2005
Examples of MarvinSpace
• surface transparency
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Slide 12
MarvinSpace — UGM 2005
Examples of MarvinSpace
• secondary structure representation
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Slide 13
MarvinSpace — UGM 2005
Future plans
• protein ribbon view• faster surface drawing (by reduction of surface triangles)• user configurable blobby molecule (potential function and blending
characteristic)• more property calculations (e.g. hydrophobic areas)• iso-surfaces• volume rendering• support for volumetric files (Gaussian cube etc)• detection of interaction sites• perception of intra molecular hydrogen bonds• protein-ligand binding energy calculation, scoring• interactive molecule construction• stereo view• navigation bar• 3d overlay• conformational search
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Slide 14
MarvinSpace — UGM 2005
Summary
• 100% java 3D molecule viewer
• Programmable (API)
• High quality rendering
• Available from June 2005
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Slide 15
MarvinSpace — UGM 2005
Máramaros köz 3/a Budapest, 1037Hungary
www.chemaxon.com
Thank you for your attention