Alignment of protein sequences using the hydrophobic core scores

Making an alignment of the amino acid sequences is an essentialstep in the prediction of an unknown protein structure by modelbuilding from the known structure of a protein of the same family.To improve the accuracy of the alignments, we introduced theconcept of hydrophobic core scores, which restrains puttinginsertions/deletions in the hydrophobic core regions of theprotein. Eight pairs of protein sequences were aligned by thismethod, and the quality of the alignments were assessed byreference to those obtained by the structural superposition.The introduction of the hydrophobic core scores derived fromthe knowledge of the tertiary structure of one of each pairresulted in an improvement of the accuracy of the alignments.The quality of the alignment was found to depend on the homologyof the protein sequences.