Alignment of protein sequences using the hydrophobic core scores

Making an alignment of the amino acid sequences is an essential step in the prediction of an unknown protein structure by model building from the known structure of a protein of the same family. To improve the accuracy of the alignments, we introduced the concept of hydrophobic core scores, which restrains putting insertions/deletions in the hydrophobic core regions of the protein. Eight pairs of protein sequences were aligned by this method, and the quality of the alignments were assessed by reference to those obtained by the structural superposition. The introduction of the hydrophobic core scores derived from the knowledge of the tertiary structure of one of each pair resulted in an improvement of the accuracy of the alignments. The quality of the alignment was found to depend on the homology of the protein sequences.