This was the subject of my MSc thesis, and has been ongoing for some time. Recently presented in a poster session at the EMBO Visualisation workshop. There have been some more exciting developments since…
Abstract as posted on the Goldsmiths Computing Mutators Research Group site:
3-5 March 2010, EMBL Heidelberg, Germany
FoldSynth is an interactive multimedia platform designed to help people understand the characteristics of protein structures. It uses a simplified model of molecular forces to give an interactive animation of the folding process. The shape of the protein is shown as a 3D visualization floating above a 2D triangular distance matrix  which provides an alternative interactive visualisation. The user adds and removes forces by interacting directly with the 3D protein or by “painting” on the 2D matrix. The shape of the protein reacts to the current set of forces with corresponding change to the distance matrix. There are simple tools to paint forces that e.g. cause the creation of alpha helices and beta sheets. Cellular automata can also operate on the distance matrix, introducing dynamic force processes. The forces can be initialized to mimic proteins loaded from a DAS server. The model includes masses and simplified forces for hydrophobicity and electric charge. The 3D visualization shows various representations (smoothed backbone, cartoon, etc.). Forces and properties (such as hydrophobicity) are mapped onto different graphical features (colour, texture, bump mapping) and sonifications. FoldSynth can recreate real protein structures, but can also create new folds which are protein-like yet fundamentally different to know protein structures. FoldSynth is a continuation of previous work we did on reading DNA data to produce visualisation of protein information which we first presented at SIGGRAPH in 2007. In this previous work we introduced a novel way to navigate backward and forward in time through the phylogenetic tree [1,2]. References:  “Using DNA to Generate 3D Organic Art Forms,” W. Latham et al., EvoMusArt 2008.  “From DNA to 3D Organic Art Forms,” W. Latham et al., SIGGRAPH 2007.  “Protein Geometry, Classification, Topology and Symmetry”, Taylor & Aszodi, IoP, 2005.