title: Prediction of catalytic residues using the variation of stereochemical properties.
abstract: In this paper, we investigate a simple protein sequence conservation measure which takes amino acid similarity into account. Instead of grouping 20 amino acids into disjoint sets in previous methods, we consider ten overlapping classes. The method is based on the assumption that a column in a multiple sequence alignment is evolved from an identical column in the evolutionary history. Two ten-dimensional vectors are constructed for each position to denote frequencies of ten classes in a column and the corresponding hypothetical identical column. Then the cosine function of the angle between these two vectors is considered as a measure of divergence of stereochemical properties at this position. This divergence, combining with other conservation scores, is used as conservation measure of the column. Finally, we evaluate our methods by identifying catalytic sites, using rank analysis criterion and receiver operator characteristic analysis criterion.
authors.affiliation: Department of Applied Mathematics, Dalian University of Technology, Dalian, People's Republic of China.
authors.forename: Yongchao
authors.initials: Y
authors.lastname: Dou
authors.forename: Xiaoqi
authors.initials: X
authors.lastname: Zheng
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D020134:Catalytic Domain; D017124:Conserved Sequence; D012372:ROC Curve; D016415:Sequence Alignment / Q000379:methods*; D018709:Statistics, Nonparametric
chemical_list: D000596:Amino Acids