Dynamic Signaling Maps™ comes with an embedded biomolecular interactions database, the Hippron Interactions Knowledge Base™. When you click the Molecular Interaction Clusters MIC/BAN icon in the DSM console a pop-up window allows you to enter database search terms, either by direct typing in the textarea or by double-clicking items in the Ontology browser:

Upon running a database search to extract a biological interaction network, also know as a "biological association network", you can optionally display clusters of molecular interactions in scalable Macromedia Flash and interactive Web3D/VRML graphics formats. For a two-dimensional diagram see screen shot below or a Flash object (Flash MX or higher viewer required):

You can interactively rearrange graphical elements in the browser window, see a demonstration in this video clip (751KB, MPEG format). This technology is now available for licensing, check out a few prototypes.

Web3D models are useful when the 2D Flash diagrams are cluttered. If molecular clustering is "tight" then the three-dimensional cluster model is compact and complex, see screen shot below or a Web3D model (VRML 97 plug-in required; try this link if you use a VRML browser rather than a plug-in), or a video clip (334KB, MPEG format). More complex and compact cluster models tend to have a spherical layout (Web3D model).

Alternatively, clustering can be "loose", in which case there are multiple, simpler 3D cluster models: