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Protein secondary structure class assignment on the basis of a new graphic representation
Author(s) -
Jia Cangzhi,
Liu Tian,
Zhang Xiangde,
Yan Shijun
Publication year - 2008
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.21865
Subject(s) - protein secondary structure , representation (politics) , basis (linear algebra) , amino acid residue , protein structure , class (philosophy) , residue (chemistry) , crystallography , chemistry , mathematics , geometry , peptide sequence , computer science , artificial intelligence , biochemistry , politics , political science , law , gene
A novel 2D representation (M‐curve) has been provided to visualize the structure information of protein secondary structure sequences: (1) end point of the curve reflects difference of amino acid residue numbers in α‐helices and β‐strands of a protein; (2) Up/down ladder‐like structures in the curve show that α‐helices/β‐strands appear sequentially in this region; (3) triangular‐like/trapeziform‐like structures of the curve show that α‐helices and β‐strands appear alternatively in this region. So from the M‐curve, a protein could be directly assigned into corresponding secondary structure class. Moreover, a new numerical descriptor, four‐component vector, is introduced and applied to cluster analysis. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009