Creating supersecondary structures with BuildBeta.

BuildBeta is a feature of the ProteinShop software designed to thoroughly sample a protein conformational space given the protein's sequence of amino acids and secondary structure predictions. It targets proteins with beta sheets because they are particularly challenging to predict due to the complexity of sampling long-range strand pairings. Here we discuss some of the most difficult targets in the recent 9th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP9) and show how BuildBeta can leverage some of the most successful methods in the category "template-free modeling" by augmenting their sampling capabilities. We also discuss ongoing efforts to improve the quality of the supersecondary structures it generates.