A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications
نویسندگان
چکیده
منابع مشابه
A Protein Structural Alphabet and Its Substitution Matrix CLESUM
By using a mixture model for the density distribution of the three pseudobond angles formed by Cα atoms of four consecutive residues, the local structural states are discretized as 17 conformational letters of a protein structural alphabet. This coarse-graining procedure converts a 3D structure to a 1D code sequence. A substitution matrix between these letters is constructed based on the struct...
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Motivation: Protein sequence world is discrete as 20 amino acids (AA) while its structure world is continuous, though can be discretized into structural alphabets (SA). In order to reveal the relationship between sequence and structure, it is interesting to consider both AA and SA in a joint space. However, such space has too many parameters, so the reduction of AA is necessary to bring down th...
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Background: Hepatitis C virus (HCV) infection is one of the most prevalent infectious diseases responsible for high morbidity and mortality worldwide. Therefore, designing new and effective therapeutics is of great importance. The aim of the current study was to construct a DNA vaccine containing structural proteins of HCV and evaluation of its expression in a eukaryot...
متن کاملSARSA: a web tool for structural alignment of RNA using a structural alphabet
SARSA is a web tool that can be used to align two or more RNA tertiary structures. The basic idea behind SARSA is that we use the vector quantization approach to derive a structural alphabet (SA) of 23 nucleotide conformations, via which we transform RNA 3D structures into 1D sequences of SA letters and then utilize classical sequence alignment methods to compare these 1D SA-encoded sequences a...
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ژورنال
عنوان ژورنال: Proteins: Structure, Function, and Bioinformatics
سال: 2006
ISSN: 0887-3585
DOI: 10.1002/prot.21087