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Recurrent Neural Network based Classification of Protein-Protein Interactions

by Dilpreet Kaur, Shailendra Singh
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International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 52 - Number 4
Year of Publication: 2012
Authors: Dilpreet Kaur, Shailendra Singh
10.5120/8188-1549

Dilpreet Kaur, Shailendra Singh . Recurrent Neural Network based Classification of Protein-Protein Interactions. International Journal of Computer Applications. 52, 4 ( August 2012), 6-11. DOI=10.5120/8188-1549

@article{ 10.5120/8188-1549,
author = { Dilpreet Kaur, Shailendra Singh },
title = { Recurrent Neural Network based Classification of Protein-Protein Interactions },
journal = { International Journal of Computer Applications },
issue_date = { August 2012 },
volume = { 52 },
number = { 4 },
month = { August },
year = { 2012 },
issn = { 0975-8887 },
pages = { 6-11 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume52/number4/8188-1549/ },
doi = { 10.5120/8188-1549 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-06T20:51:24.014066+05:30
%A Dilpreet Kaur
%A Shailendra Singh
%T Recurrent Neural Network based Classification of Protein-Protein Interactions
%J International Journal of Computer Applications
%@ 0975-8887
%V 52
%N 4
%P 6-11
%D 2012
%I Foundation of Computer Science (FCS), NY, USA
Abstract

Proteomics is an attempt to describe or explain biological state and qualitative and quantitative changes of protein content of cells and extracellular biological materials under different conditions to further understand biological processes. Protein-Protein interaction prediction and classification is a very important task. Prediction and classification of protein-protein interactions can help in improving the understanding of diseases and can provide the basis for new therapeutic approaches. In this work a model is proposed to classify protein-protein interactions. Jordan Recurrent Neural Network is used to classify the protein-protein interactions. The model developed gives 97. 25% of accuracy which is 8. 7% more than Back-Propagation Neural Network.

References
  1. Agarwal S, Singh H et. al. "Identification of Mannose Interacting Residues Using Local Composition", PLoS ONE, 2011.
  2. Jordan, M. I. , "Serial Order: A parallel Distributed Processing Approach", Tech. rep. Report, pp. 86-104, 1986.
  3. Zhiqiang Ma, Chunguang Zhou et. al. , "Predicting Protein-Protein Interactions Based on BP Neural Network" IEEE Conference on Bioinformatics and Biomedicine Workshops, pp. 3-7, 2007.
  4. Lishuang Li, Linmei Jing et. al. , "Protein-Protein Interaction Extraction from Biomedical Literatures Based on Modified SVM-KNN", IEEE International Conference on Natural Language Processing and knowledge Engineering, pp. 1-7, 2009.
  5. Hong-Wei Liu, "Protein-Protein Interaction Detection by SVM from Sequence Information", The Third International Symposium on Optimization and Systems Biology, pp. 198-206, 2009.
  6. Cathy H. Wu, Rolf Apweiler, Amos Bairoch et. al. , "The Universal Protein Resource (UniProt): an expanding universe of protein information", Nucleic Acids Research,vol. 34, pp. 187–191, 2006.
  7. Amos Bairoch, Rolf Apweiler, "The SWISS-PROT protein sequence data bank and its supplement TrEMBL", Nucleic Acids Research, vol. 25, no. 1, pp. 31–36, 1997.
  8. Helen M. Berman, John Westbrook et. al. , "The Protein Data Bank", Nucleic Acid Research, vol. 28, no. 1, pp. 235-242, 2000.
  9. Suraj Peri, J. Daniel Navarro, Troels Z. Kristiansen, Ramars Amanchy et. al. , "Human protein reference database as a discovery resource for proteomics", Nucleic Acids Research, vol. 32, pp. 497-501, 2004.
  10. Robert D. Finn, John Tate et. al. , "The Pfam protein families database", Nucleic Acids Research, vol. 36, pp. 281–288, 2008.
  11. Amelie Stein, Robert B. Russell and Patrick Aloy, "3did: interacting protein domains of known three-dimensional structure", Nucleic Acids Research, vol. 33, pp. 413–417, 2005.
  12. Pawel Smialowski, Philipp Page et. al. , "The Negatome database: a reference set of non-interacting protein pairs", Nucleic Acids Research, pp. 1–5, 2009.
  13. Kabsch W, Sander C, "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features", Biopolymers, pp. 2577-2637, 1983.
  14. Gajendra PS Raghava, Joon H Han, "Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein", BMC Bioinformatics, 2005.
  15. Christoph Bergmeir, José M. Benítez, "Neural Networks in R using the Stuttgart Neural Network Simulator", Repository CRAN, 2012.
  16. W. N. Venables, D. M. Smith, "R: A Programming Environment for Data Analysis and Graphics", Version 2. 15. 0, 2012.
  17. http://en. wikipedia. org/ wiki /Protein%E2%80%93prot ein_interaction_prediction
  18. http://en. wikipedia. org/wiki/Bioinformatics
  19. http://en. wikipedia. org/wiki/Proteomics
  20. http://en. wikipedia. org/wiki/Protein%E2%80%93protein interaction
  21. http://en. wikipedia. org/wiki/Pseudo_amino_acid_compo -sition
  22. http://www. heatonresearch. com/wiki/Jordan_Neural_Net -work
Index Terms

Computer Science
Information Sciences

Keywords

Protein-Protein Interactions Jordan Recurrent Neural Network Back-Propagation (BP) Neural Network SVM SVM-KNN Amino Acid Composition

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