Premium
The influence of tertiary structure on secondary structure prediction
Author(s) -
Garratt Richard C.,
Taylor William R.,
Thornton Janet M.
Publication year - 1985
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/0014-5793(85)80874-7
Subject(s) - protein secondary structure , hydrogen bond , amino acid residue , protein structure prediction , protein tertiary structure , chemistry , beta sheet , crystallography , protein structure , residue (chemistry) , mathematics , biological system , biology , peptide sequence , biochemistry , molecule , organic chemistry , gene
The secondary structure prediction algorithm of Garnier et al. [(1978) J. Mol. Biol. 120, 97‐120] has been used for 16 proteins whose structures are dominated by β‐sheet. Comparisons of the predicted structures with those defined by the algorithm of Kabch and Sander [(1983) Biopolymers 22, 2577‐2637] shows that for β‐sheet residues, the quality of prediction falls markedly with increasing residue accessibility. 2 sub‐classes of β‐residues have been distinguished on the basis of hydrogen bonding patterns, and the distribution of amino acid types within each sub‐class found to be quite different. Accordingly, Chou and Fasman P β ‐type parameters for these previously indistinguished states have been derived.