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Article
Protein Secondary Structure Prediction using Parallelized Rule Induction from Coverings
Proceedings of the World Academy of Science, Engineering and Technology
  • Leong Lee
  • Cyriac Kandoth
  • Jennifer Leopold, Missouri University of Science and Technology
  • Ronald L. Frank, Missouri University of Science and Technology
Abstract

Protein 3D structure prediction has always been an important research area in bioinformatics. In particular, the prediction of secondary structure has been a well-studied research topic. Despite the recent breakthrough of combining multiple sequence alignment information and artificial intelligence algorithms to predict protein secondary structure, the Q3 accuracy of various computational prediction algorithms rarely has exceeded 75%. In a previous paper [1], this research team presented a rule-based method called RT-RICO (Relaxed Threshold Rule Induction from Coverings) to predict protein secondary structure. The average Q3 accuracy on the sample datasets using RT-RICO was 80.3%, an improvement over comparable computational methods. Although this demonstrated that RT-RICO might be a promising approach for predicting secondary structure, the algorithm's computational complexity and program running time limited its use. Herein a parallelized implementation of a slightly modified RT-RICO approach is presented. This new version of the algorithm facilitated the testing of a much larger dataset of 396 protein domains [2]. Parallelized RTRICO achieved a Q3 score of 74.6%, which is higher than the consensus prediction accuracy of 72.9% that was achieved for the same test dataset by a combination of four secondary structure prediction methods [2].

Department(s)
Computer Science
Second Department
Biological Sciences
Keywords and Phrases
  • Data Mining,
  • Parallelization,
  • Protein Secondary Structure Prediction
Document Type
Article - Journal
Document Version
Final Version
File Type
text
Language(s)
English
Rights
© 2009 World Academy of Science, Engineering and Technology, All rights reserved.
Creative Commons Licensing
Creative Commons Attribution-Share Alike 4.0
Publication Date
12-1-2009
Publication Date
01 Dec 2009
Disciplines
Citation Information
Leong Lee, Cyriac Kandoth, Jennifer Leopold and Ronald L. Frank. "Protein Secondary Structure Prediction using Parallelized Rule Induction from Coverings" Proceedings of the World Academy of Science, Engineering and Technology Vol. 36 (2009) p. 388 - 394 ISSN: 2010-376X
Available at: http://works.bepress.com/ronald-frank/10/