Assessing the reliability of sequence similarities detected through hydrophobic cluster analysis

Hydrophobic cluster analysis (HCA) has long been used as a tool to detect distant homologies between protein sequences, and to classify them into different folds. However, it relies on expert human intervention, and is sensitive to subjective interpretations of pattern similarities. In this study, we describe a novel algorithm to assess the similarity of hydrophobic amino acid distributions between two sequences. Our algorithm correctly identifies as misattributions several HCA-based proposals of structural similarity between unrelated proteins present in the literature. We have also used this method to identify the proper fold of a large variety of sequences, and to automatically select the most appropriate structure for homology modeling of several proteins with low sequence identity to any other member of the protein data bank. Automatic modeling of the target proteins based on these templates yielded structures with TM-scores (vs. experimental structures) above 0.60, even without further refinement. Besides enabling a reliable identification of the correct fold of an unknown sequence and the choice of suitable templates, our algorithm also shows that whereas most structural classes of proteins are very homogeneous in hydrophobic cluster composition, a tenth of the described families are compatible with a large variety of hydrophobic patterns. We have built a browsable database of every major representative hydrophobic cluster pattern present in each structural class of proteins, freely available at http://www2.ufp.pt/ pedros/HCA_db/index.htm.