Improved alignment of weakly homologous protein sequences using structural information

Protein sequence alignments can be unproved when at least oneof the proteins to be aligned has a known 3-D structure. Inthis work, geometrical constraints extracted from the targetfold are evaluated in independent units that deal with complementarystructural features. This information is used to set up mutationtables specific to the locally observed structural environments.The resulting partial evaluations are then combined linearlyinto a global function which is optimized by dynamic programming.Eventually, a score based on tertiary interactions can be usedas a selection criterion to discriminate among a set of suboptimalalignments. The relevance of the scores given by each unit istested on a representative set of protein families. Finally,a method for combining the different scores is described andits efficiency is evaluated on a few pairs of weakly homologousproteins.