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

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Presentation transcript:

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

Slide 2 MarvinSpace UGM 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

Slide 3 MarvinSpace UGM 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)

Slide 4 MarvinSpace UGM 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

Slide 5 MarvinSpace UGM Examples of MarvinSpace atoms are spheres, not ragged polyhedra. Proper lights and reflections, not a uniform lit ball placed at every atom position.

Slide 6 MarvinSpace UGM Examples of MarvinSpace Optional depth cueing (fog effect)

Slide 7 MarvinSpace UGM Examples of MarvinSpace smooth surfaces no missing or odd triangles

Slide 8 MarvinSpace UGM Examples of MarvinSpace fast, novel algorithm, not the common analytic approach accurate saddle for three and more nearby atoms

Slide 9 MarvinSpace UGM Examples of MarvinSpace Blobby molecule: a novel approach to surface representation easy to configure to obtain smooth surfaces

Slide 10 MarvinSpace UGM Examples of MarvinSpace antialiasing

Slide 11 MarvinSpace UGM Examples of MarvinSpace surface transparency

Slide 12 MarvinSpace UGM Examples of MarvinSpace secondary structure representation

Slide 13 MarvinSpace UGM 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

Slide 14 MarvinSpace UGM Summary 100% java 3D molecule viewer Programmable (API) High quality rendering Available from June 2005

Slide 15 MarvinSpace UGM Máramaros köz 3/a Budapest, 1037 Hungary Thank you for your attention