S curve, a graphic representation of protein secondary structure sequence and its applications.
A secondary structure sequence is a symbolic string composed of three kinds of letters, indicating the helix, strand, and coil (including turns), respectively. A graphic representation for this abstract symbolic sequence is proposed here, called the S curve. The S curve is the unique representation for a given secondary structure sequence in the sense that the sequence and the S curve can be uniquely determined from the other. Therefore, the S curve contains all the information that the secondary structure sequence contains. Different geometrical properties of the S curve are studied in details, which reflect the basic characteristics of the secondary structure sequences. The S curves are used to display, analyze, and compare the secondary structure sequences. Detailed application examples are presented. One advantage of the S curve methodology is that the main patterns of a given secondary structure sequence can be grasped quickly in a perceivable form. This is particularly useful in the cases in which longer sequences are involved and structures of proteins are unknown.
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Department of Physics, Tianjin University, Tianjin 300072, China. ctzhang@tju.edu.cn
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D000595:Amino Acid Sequence; D008958:Models, Molecular; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
D010455:Peptides; D011506:Proteins