Protein Secondary Structure Prediction using Rule Induction from Coverings
With the increase of data from genome sequencing projects comes the need for reliable and efficient methods for the analysis and classification of protein motifs and domains. Experimental methods currently used to determine protein structure are accurate, yet expensive both in terms of time and equipment. Therefore, various computational approaches to solving the problem have been attempted, although their accuracy has rarely exceeded 75%. In this paper, a rule-based method to predict protein secondary structure is presented. This method uses a newly developed data-mining algorithm called RT-RICO (Relaxed Threshold Rule Induction from Coverings), which identifies dependencies between amino acids in a protein sequence, and generates rules that can be used to predict secondary structures. The average prediction accuracy on sample data sets, or Q3 score, using RT-RICO was 80.3%, an improvement over comparable computational methods.
L. Lee et al., "Protein Secondary Structure Prediction using Rule Induction from Coverings," Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (2009, Nashville, TN), pp. 79-86, Institute of Electrical and Electronics Engineers (IEEE), Apr 2009.
The definitive version is available at http://dx.doi.org/10.1109/CIBCB.2009.4925711
2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '09 (2009: Mar. 30-Apr. 2, Nashville, TN)
Keywords and Phrases
Amino acids; Protein sequence; Protein engineering; Probability; Genomics; Bioinformatics; Induction generators; Accuracy; Nuclear magnetic resonance; Neural networks
International Standard Book Number (ISBN)
Article - Conference proceedings
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