Abstract
Inter-dependent mutations among residue sites in a protein structure are often an indication of spatial proximity of these residues, and this type of information is being used to predict protein structures. Mutations at one site alone can be deleterious for the protein because of these inter-dependencies (evolutionary correlations). In order to produce functional proteins, one or more sites need to mutate in a coordinated way. Most existing sequence alignment algorithms used single amino acid substitutions to make alignments.
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