Sanyukta Chetia
Kandarpa Kumar Sarma
ABSTRACT
One of the most important macromolecule found in every organism is protein. It performs a wide variety of functions. Improper functioning of certain proteins leads to various abnormalities in the human body. The proper functioning of a protein is determined by its structure. Hence, protein structure prediction is in great demand in the field of bio-informatics. Along with the experimental methods, now-a-days soft computational tools are also used to predict the structure of a protein. The Artificial Neural Network (ANN) is one such tool which is used for structure prediction of proteins. Different 3D images of proteins are collected from Protein Data Bank (PDB) [1]. The dimensions of these images are very large. In this paper, Self-Organizing Map (SOM) is used to reduce the dimensions of the images of proteins which are next used as ANN's inputs for training, enabling it to recognize various structures of protein. The proposed SOM based approach is found to be superior in terms of computational complexity compared to Principal Component Analysis (PCA) based method.
- Webpages-Protein Data Bank (http://www.rcsb.org/pdb/home/home.do),Protein Structure (http://en.wikipedia.org/wiki/Protein_structure), Self-organizing map (http://en.wikipedia.org/wiki/Self-organizing_map), Self- Organizing Maps (http://davis.wpi.edu/~matt/courses/soms/), Principal Component Analysis (http://en.wikipedia.org/wiki/Principal_component_analysis).Google Scholar
- H. Bordoloi and K. K. Sarma, "Protein Structure Prediction using Artificial Neural Network", International Journal of Computer Applications on Electronics, Special Issue of International Conference on Electronics, Information and Communication Engineering - ICEICE No.3, Dec 2011.Google Scholar
- H. Bordoloi and K. K. Sarma, "Protein Structure Prediction Using Multiple Artificial Neural Network Classifier", Studies in Computational Intelligence, 2012, Volume 395, Soft Computing Techniques in Vision Science, Pages 137--146, Springer Verlag, Berlin, 2012.Google ScholarCross Ref
- S. Chetia and K. K. Sarma, "PCA and SOM based Dimension Reduction Techniques for Quaternary Protein Structure Prediction", communicated to International Journal of Computer Applications, IJCA-2012.Google Scholar
- S. Chetia and K. K. Sarma, "Protein Structure Prediction using Certain Dimension Reduction Techniques and ANN", communicated to 3rd International Conference on Computer and Communication Technology, ICCCT-2012, Allahabad, 2012.Google Scholar
- S. Chetia and K. K. Sarma, "Soft Computational Approaches for Protein Structure Prediction using Certain Image Processing Techniques", communicated to International Conference on Electronics and Communication Engineering-ICECE-2012, Guwahati, 2012.Google Scholar
- S N Sivanandam, S Sumathi and S N Deepa, "Introduction to Neural Networks using MATLAB", Tata McGraw-Hill Education, New Delhi, 2006.Google Scholar
- S. Kumar, "Neural Networks- A Classroom Approach", Tata McGraw-Hill, New Delhi, 2011Google Scholar
Index Terms
- SOM based dimension reduction techniques for quaternary protein structure prediction
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