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OJB
Online Journal of
Bioinformatics
Volume 5:13-22, 2004.
Prediction of Protein
Homo-oligomers by Incorporating Quasi-Sequence-Order Effect.
Zhang SW,
Pan Q, Zhang HC, Wu YH, Shi JU.
Department of Automatic Control,
ABSTRACT
Zhang SW
Pan Q, Zhang HC, Wu YH, Shi J,U Prediction of Protein Homo-oligomers by
Incorporating Quasi-Sequence-Order Effect, Onl J Bioinform., 5:13-22, 2004. A method of extracting features from
protein primary sequences, incorporating quasi-sequence-order effects, was used
to predict protein homodimers, homotrimers, homotetramers and homohexamers.
It was found that overall predictive accuracy based on amino acid composition
and sequence-order-coupling numbers with one-versus-rest method was 81.25%, or
3.89% higher than that based solely on amino acid composition under identical
conditions. With the same attribute parameter set at CSO, composed of amino
acids and sequence-order-coupling numbers, the overall predictive accuracy of
all-versus-all method was 13.14% higher than that of one-versus-rest method.
These results show that the method of extracting attribute vector from protein
primary sequences by incorporating Quasi-Sequence-Order Effect is feasible and
the primary sequences of homo -oligomers contain protein quaternary
information. The results suggest that all-versus-all multi-class classification
methods may be effective for predicting the higher homo-oligomers.
KEY WORDS: sequence-order-coupling numbers; all-versus-all;
one-versus-rest; homo -oligomers
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