dorsal/arxiv
View SchemaAmino acid substitution matrices for protein conformation identification
| Authors | Xin Liu, Wei-Mou Zheng |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0406032 |
| URL | https://arxiv.org/abs/q-bio/0406032 |
Abstract
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.
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"abstract": "Methods for alignment of protein sequences typically measure similarity by\nusing substitution matrix with scores for all possible exchanges of one amino\nacid with another. Although widely used, the matrices derived from homologous\nsequence segments, such as Dayhoff\u0027s PAM matrices and Henikoff\u0027s BLOSUM\nmatrices, are not specific for protein conformation identification. Using a\ndifferent approach, we got many amino acid segment blocks. For each of them,\nthe protein secondary structure is identical. Based on these blocks, we have\nderived new amino acid substitution matrices. The application of these matrices\nled to marked improvements in conformation segment search and homologues\ndetection in twilight zone.",
"arxiv_id": "q-bio/0406032",
"authors": [
"Xin Liu",
"Wei-Mou Zheng"
],
"categories": [
"q-bio.BM"
],
"title": "Amino acid substitution matrices for protein conformation identification",
"url": "https://arxiv.org/abs/q-bio/0406032"
},
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