Just saw an interesting article "CellPAINT: Interactive Illustration of Dynamic Mesoscale Cellular Environments" DOI.

Integrative computational modeling is currently the method of choice for studying the detailed mesoscale molecular structure of cellular environments. However, current methods are highly compute intensive and require extensive and diverse domain knowledge. We have developed an interactive mesoscale illustration method, cellPAINT, that allows non-expert users to create mesoscale models that integrate a variety of biological data. CellPAINT uses the approach of popular digital painting software, providing users with a palette of “brushes” to paint molecules and infrastructure into a mesoscale scene, and coloring tools and visual filters to customize the rendering. CellPAINT also incorporates a variety of mesoscale properties, such as an interactive temperature slider that controls diffusive motion and interaction of proteins within membranes. The current release allows creation of scenes with an HIV virion, blood plasma, and a simplified T-cell.

The software can be downloaded from Sourceforge