The comparison of structures and sequences: alignment, searching and the detection of common folds

Describes an approach to the comparison and analysis of protein sequences and three-dimensional (3-D) structures. This includes the alignment of structures (using a combination of a genetic algorithm, dynamic programming and least-squares minimization) the alignment of sequences, the search for related structures/sequences and the detection of common folds. These latter procedures are grounded upon the structural alignment of many protein families and the analysis of amino acid substitutions at matched positions within these alignments. The authors consider the local physico-chemical environment within the structure but also those residue-residue and side-chain to main-chain contacts that may occur at a distance along the sequence.<>