Fold recognition amino acid substitution

For fold recognition, the amino acid substitution matrix can be replaced by a 3D-ID substitution matrix (scoring table) computed from a database of known structures and sets of sequence-structure alignments (Bowie et al., 1991). Recently, the matrix has been further extended to include predicted secondary structure of the sequence using a H3P2 matrix (Rice Eisenberg, 1997). The 3D-ID substitution matrix allows one to match the amino acid residues (and/or their secondary structure prediction) with structural (environmental) classes. 

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