1 Miklós Vargyas, Judit Papp May, 2005 MarvinSpace – live demo

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Miklós Vargyas, Judit Papp

May, 2005

MarvinSpace – live demo

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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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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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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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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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MarvinSpace — UGM 2005

Examples of MarvinSpace

• Optional depth cueing (fog effect)

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MarvinSpace — UGM 2005

Examples of MarvinSpace

• smooth surfaces

• no missing or odd triangles

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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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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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MarvinSpace — UGM 2005

Examples of MarvinSpace

• antialiasing

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MarvinSpace — UGM 2005

Examples of MarvinSpace

• surface transparency

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MarvinSpace — UGM 2005

Examples of MarvinSpace

• secondary structure representation

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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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MarvinSpace — UGM 2005

Summary

• 100% java 3D molecule viewer

• Programmable (API)

• High quality rendering

• Available from June 2005

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MarvinSpace — UGM 2005

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info@chemaxon.com

www.chemaxon.com

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