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Application for Understanding Protein Simulations
"PPV interface" Distance correlation matrix. Upper triangle additionally marks close contacts (less than 6.5 angstroms) between amino acid residues. A close contact between two sheet residues (orange) has been picked.

Two-dimensional histogram of phi vs. psi angles (yellow indicates bins with more residues with that pair of angles). Bins containing picked residues are marked by red.

plot of phi and psi vs. residue number. Picked residues are marked.
In the screen shot shown here, the user has selected a pair of amino acid residues in the upper right distance correlation matrix (within the orange band, shown with a circle). This pair of residues is automatically indicated by a pair of green spheres in the three-dimensional view, along with an indication of the distance between them, and also displayed in views showing the phi and psi angles which are correlated with the particular local protein structure.

This application is available for download from IBM alphaWorks.

"Case Study: An Environment for Understanding Protein Simulations Using Game Graphics", Donna Gresh and Frank Suits,Proceedings IEEE Visualization 2001