title: Several appropriate background distributions for entropy-based protein sequence conservation measures.
abstract: Amino acid background distribution is an important factor for entropy-based methods which extract sequence conservation information from protein multiple sequence alignments (MSAs). However, MSAs are usually not large enough to allow a reliable observed background distribution. In this paper, we propose two new estimations of background distribution. One is an integration of the observed background distribution and the position-specific residue distribution, and the other is a normalized square root of observed background frequency. To validate these new background distributions, they are applied to the relative entropy model to find catalytic sites and ligand binding sites from protein MSAs. Experimental results show that they are superior to the observed background distribution in predicting functionally important residues.
authors.affiliation: School of Mathematical Science, Dalian University of Technology, Dalian 116024, PR 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: D000595:Amino Acid Sequence; D020134:Catalytic Domain; D017124:Conserved Sequence; D019277:Entropy; D008024:Ligands; D012372:ROC Curve; D020539:Sequence Analysis, Protein
chemical_list: D008024:Ligands