Visualization and interpretation of computational models

COMP 204

Kevin Schmidt, kevin@eyesopen.com, Brian Kelley, kelley@eyesopen.com, 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.