Amino acid sequence homology applied to the prediction of protein secondary structures, and joint prediction with existing methods.
The assumption that homologous segments in different proteins may share a similar conformation is applied to the prediction of secondary structures in proteins. Sequences homologous to a target protein are searched, without allowing any gap, and compared against a number of reference proteins of known three-dimensional structure, and then a conformational state (alpha, beta or coil) for each residue of the protein is predicted by looking at the secondary structure of corresponding homologous segments. This prediction is done in a statistical rather than 'deterministic' way, by assigning the most probable conformation state among homologous data to each residue site of a target protein. A test application for 22 sample proteins yields 60% correctness on the average, a better value in comparison with two other existing methods. Joint prediction combining three methods into one is shown to increase the reliability up to 70%, when only the regions identically predicted with the three methods are taken into account. Application of the present method to 10 proteins of unknown structure is demonstrated.
Nishikawa
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K
Ooi
T
T
D000595:Amino Acid Sequence; D000818:Animals; D011487:Protein Conformation; D011506:Proteins; D012689:Sequence Homology, Nucleic Acid; D013329:Structure-Activity Relationship; D014598:Uteroglobin
D011506:Proteins; D014598:Uteroglobin