Amino acid substitution matrices for protein conformation identification
نویسندگان
چکیده
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. PACS number(s): 87.10.+e,02.50.-r
منابع مشابه
An Amino Acid Substitution Matrix for Protein Conformation Identification
Amino acid substitution matrices play an essential role in protein sequence alignment, a fundamental task in bioinformatics. Most widely used matrices, such as PAM matrices derived from homologous sequences and BLOSUM matrices derived from aligned segments of PROSITE, did not integrate conformation information in their construction. There are a few structure-based matrices, which are derived fr...
متن کاملAmino acid distance matrices and classifications for different protein secondary structure
The property of an amino acid is different according to the variation of protein secondary structure. Each central amino acid corresponds to several conditional probability distributions of amino acid on the specific positions surrounding it. Based on this property, we get amino acid distance matrices for helix, sheet, coil and turn conformation. It is observed that, for different protein secon...
متن کاملPosition Dependent and Independent Evolutionary Models Based on Empirical Amino Acid Substitution Matrices
Evolutionary models measure the probability of amino acid substitutions occurring over different evolutionary distances. We examine various evolutionary models based on empirically derived amino acid substitution matrices. The models are constructed using the PAM and BLOSUM amino acid substitution matrices. We rescale these matrices by raising them to powers to model substitution patterns that ...
متن کاملA Transition Probability Model for Amino Acid Substitutions from Blocks
Substitution matrices have been useful for sequence alignment and protein sequence comparisons. The BLOSUM series of matrices, which had been derived from a database of alignments of protein blocks, improved the accuracy of alignments previously obtained from the PAM-type matrices estimated from only closely related sequences. Although BLOSUM matrices are scoring matrices now widely used for pr...
متن کاملAmino Acid Substitution Matrices Estimated by Maximum Likelihood
The present work describes protrates, a program that estimates amino acid substitution matrices and among-site substitution rates based on their likelihood for a given tree topology and a dataset of aligned proteins. The issue of producing maximum likelihood (ML) rate matrices over protein data have been adressed under the framework of general-purpose unbiased substitution matrices [1, 9], sinc...
متن کامل