A new catalog of protein beta-sheets

Systematic protein folding studies depend on protein three-dimensional structure annotation, the assignment of amino acid structural types from atomic coordinates. Significant stabilizing factors between adjacent beta-sheet peptide chains have recently been characterized and were not considered during the development of previously published annotation methods. To produce an accurate beta-sheet domain catalog and to encompass the full beta-sheet spectacle, we developed a method, beta-Spider, which evaluates a packing energy between adjacent peptide chains in accordance with the newly discovered stabilizing factors. While considering important energetic factors, our approach also minimizes the use of subjective criteria, such as (phi,psi) boundaries and sets of H-bonding motifs that are used in other existing methods. As a result of the application of beta-Spider to a set of available high-resolution X-ray crystal structures, we present here a new beta-sheet catalog that differs considerably from the one produced by the most acclaimed DSSP method. The catalog includes new H-bonding motifs that were never reported.