Comparative visualization of protein structure-sequence alignments

Protein fold recognition (threading) involves the prediction of a protein's three-dimensional shape based on its similarity to a protein whose structure is known. Fold predictions are low resolution; no effort is made to rotate the protein's component amino acid side chains into their correct spatial orientations. Rather, the goal is to recognize the protein family member that most closely resembles the target sequence of unknown structure and to create a sensible alignment of the target to the structure (i.e., a structure-sequence alignment). To complement this structure prediction method the authors have implemented a low resolution molecular graphics tool. Since amino acid side chain orientation is not relevant in fold recognition, amino acid residues are represented by abstract shapes or glyphs much like Lego/sup TM/ blocks. They also borrow techniques from comparative streamline visualization to provide clean depictions of the entire protein structure model. By creating a low resolution representation of protein structure, they are able to approximately double the amount of information on the screen. This implementation also possesses the advantage of eliminating distracting and possibly misleading visual clutter resulting from the mapping of protein alignment information onto a high resolution display of a known structure.