Amino acid substitution matrices for protein conformation identification
  Methods for alignment of protein sequences typically measure similarity by using substitution matrix with scores for all possible exchanges of one amino acid with another. Although widely used, the matrices derived from homologous sequence segments, such as Dayhoff's PAM matrices and Henikoff's BLOSUM matrices, are not specific for protein conformation identification. Using a different approach, we got many amino acid segment blocks. For each of them, the protein secondary structure is identical. Based on these blocks, we have derived new amino acid substitution matrices. The application of these matrices led to marked improvements in conformation segment search and homologues detection in twilight zone. 
Xin Liu, Wei-Mou Zheng