Scoring matrix based on similarity of protein backbone dihedral angles

• Autorzy: Pokuta W.
• Języki publikacji: EN

Abstrakty

EN

The article describes the results of studies on the similarity of protein structures generated by the sequences differing by only one amino acid residue. On this basis, the table of amino acid residue similarities has been determined. Similar residue sequences should generate similar protein structures – on this basis act such classification systems as SCOP and CATH. These systems detect the existence of domains of different lengths in the sequences. These domains are characteristic for proteins which exist in organisms. Synthesized proteins are not related to any other proteins and may contain domains that can not be classified by traditional methods. The solution to this problem may be to analyzing all the possible combinations of amino acid residues and observation of secondary structures generated by this sequence in exising proteins. Analyzing the structural differences in the sequences differing only by one amino acid residue gives information on the structural similarity of these amino acids. The task of analyzing all possible combinations of amino acid sequence is possible only for short stretches, because for longer stretches the same sequence cannot be found in the existing databases. So the second question is: how long the sequence should be analyzed in order to enable determining the local backbone structure. For this purpose, segments of known proteins with a length of 3 and 5 amino acid residues are analyzed.

Słowa kluczowe

EN

proteins; comparative modeling; substitution matrix; protein-scoring matrix; protein secondary structure; protein tertiary structure; sequence similarity; structure similarity

PL

białka; modelowanie porównawcze; matryca substytucji; punktacja białek matrycy; struktura białka wtórnego; struktura trzeciorzędowa białka; podobieństwo sekwencji; podobieństwo struktury

• Wydawca: Komisja Informatyki Polskiej Akademii Nauk, Oddział w Gdańsku
• Czasopismo: Metody Informatyki Stosowanej
• Rocznik: 2011
• Tom: nr 3
• Strony: 137--149
• Opis fizyczny: Bibliogr. 42 poz., rys., tab.

Twórcy

autor

Pokuta W.

• Politechnika Opolska, Wydział Elektrotechniki, Automatyki i Informatyki

Bibliografia

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