Journal
NEUROCOMPUTING
Volume 148, Issue -, Pages 409-419Publisher
ELSEVIER SCIENCE BV
DOI: 10.1016/j.neucom.2014.06.001
Keywords
Protein secondary structure prediction; Protein structural class; Lempel-Ziv algorithm; K-NN classification algorithm; Fuzzy k-nearest-neighbor algorithm; Field programmable gate arrays
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Funding
- Universiti Sains Malaysia Postgraduate Incentive Grant [1001/PELECT/8023013]
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Correct prediction of protein secondary structural classes is vital for the prediction of tertiary structures and understanding of their function. Most of the prediction algorithms require lengthy computation time. Nearest neighbor - complexity distance measure (NN-CDM) algorithm was one of the significant prediction algorithms using Lempel-Ziv (LZ) complexity-based distance measure, but it is slow and ineffective in handling uncertainties. To solve the problems, we propose fuzzy NN-CDM (FKNN-CDM) algorithm that incorporates the confidence level of prediction results and enhance the prediction process by designing hardware architecture that implements the proposed algorithm in an FPGA board. Highest average prediction accuracies for Z277 and 25PDB datasets using proposed algorithm are 84.12% and 47.81% respectively, with 15 times faster computation using an Altera DE2-115 FPGA board. (C) 2014 Elsevier B.V. All rights reserved.
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