Visualization and interpretation of computational models

COMP 204

Kevin Schmidt,, Brian Kelley,, Joe Corkery, Jon Christopher, and Robert Tolbert. OpenEye Scientific Software, American Twine Office Park, 222 Third Street, Suite 3120, Cambridge, MA 02142
VIDA2 is a next generation visualizer for computational models. It provides tight integration of 2D depiction, 3D visualization and spreadsheet data built on a solid cheminformatics infrastructure (OEChem) and offering python scripting for custom applications. The central divergence from VIDA1 is the facility to view and operate upon multiple molecules at once, either through a multi-pane view or the redesigned list manager. Many thousands of multi-conformer molecules can be handled, either alone or in the context of a protein active site. Grid and surfaces are handled as additional data classes, with support for many different formats and operations. Grids, with such properties as electrostatics and electron-density, can be viewed with real-time iso-contouring. Surfaces may be manipulated by property or by hand. Chemical handing includes bond and residue perception, substructure searching and SMILES representations. VIDA2 runs on all major platforms.