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Reseach Article
Protein Function Prediction using Nearer Neighbor Proteins Interactions
| International Journal of Computer Applications |
| Foundation of Computer Science (FCS), NY, USA |
| Volume 186 - Number 17 |
| Year of Publication: 2024 |
| Authors: Saima Khan, Saifuddin Md. Tareeq |
10.5120/ijca2024923555
|
Saima Khan, Saifuddin Md. Tareeq . Protein Function Prediction using Nearer Neighbor Proteins Interactions. International Journal of Computer Applications. 186, 17 ( Apr 2024), 15-22. DOI=10.5120/ijca2024923555
Abstract
Protein is one of the most important elements of life. It is responsible for structuring organs, regulating various activities of human body, transporting materials throughout the body etc.Wet lab based experiments for determining protein functions are time consuming, difficult and expensive. Computational methods have got high demands in predicting the functions of proteins because these methods save a significant amount of time and are easier and less expensive than wet lab-based experiments. There are various approaches of predicting protein functions using computational methods. In this study, a novel idea has been proposed to predict the functions of proteins using protein-protein interaction network. This method is based on k-means clustering algorithm, nearer neighbor proteins functions and also the common neighbor proteins functions.
References
- Emrah Akkoyun and Tolga Can. ”Parallelization of the functional ow algorithm for prediction of protein function using protein-protein interaction networks”. In: (2011), pp. 56-62.
- Tania Chatterjee, piyali Chatterji, Shubhadip Basu, Mahantapas Kundu, Mita Nasipuri, ”Protein function by minimum distance classifier from protein interaction network”, 2012, pp. 588-591.
- Haretsugu Hishigaki, Kenta Nakai, Toshihide Ono, Akira Tanigami, Toshihisa Takagi, ”Assessment of prediction accuracy of protein function fromproteinprotein interaction data”. In: Yeast 18.6 (2001), pp. 523-531.
- Ulas Karaoz, T. M. Murali, Stan Letovsky, Yu Zheng, Chunming Ding, Charles R. Cantor, and Simon Kasif, ”Wholegenome annotation by using evidence integration in functionallinkage networks”. In: Proceedings of the National Academy of Sciences of the United States of America 101.9 (2004), pp. 2888-2893.
- Peipei Li, Lyong Heo, Meijing Li, Keun Ho Ryu, Gouchol Pok, ,”Protein function prediction using frequent patterns in proteinprotein interaction networks”, 2011, pp. 1616-1620.
- Chuan Lin, Daxin Jiang, and Aidong Zhang. ”Prediction of protein function using common neighbors in protein-protein interaction networks”. In: (2006), pp. 251-260.
- Elena Nabieva, Kam Jim, Amit Agarwal, Bernard Chazelle and Mona Singh, ”Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps”. In: Bioinformatics 21.suppl 1 (2005), pp. i302-i310.
- String. url: string-db.org.
- Uniprot. url: uniprot.org
- Arvind Kumar Tiwari and Rajeev Srivastava, ”A survey of computational intelligence techniques in protein function prediction”. In: International journal of proteomics 2014 (2014).
- Alexei Vazquez, Alessandro Flammini, Amos Maritan, Alessandro Vespignani. ”Global protein function prediction from protein-protein interaction networks”. In: Nature biotechnology 21.6 (2003), pp. 697-700.
- Wei Xiong, Hui Liu, Jihong Guan, Shuigeng Zhou, ”Protein function prediction by collective classification with explicit and implicit edges in protein-protein interaction networks”. In: BMC bioinformatics 14.12 (2013), S4.
- Dengdi Sun, Maolin Hu, ”Determining Protein Function by Protein-protein Interaction Network”, 2007, IEEE.
- Young-Rae Cho, Aidong Zhang, Discovering frequent patterns of functional associations in protein interaction networks for function prediction, IEEE International Conference on Bioinformatics and Biomedicine, 2008.
- Qingshan Ni1, Zhengzhi Wang1, Qingjuan Han2, Gangguo Li1, Xiaomin Wang1, Guangyun Wang1, ”Using logistic regression method to predict protein function from proteinprotein interaction data”, IEEE, 2009.
- Young-Rae Cho, Member, IEEE, and Aidong Zhang, ”Predicting Protein Function by Frequent Functional Association Pattern Mining in Protein Interaction Networks”, IEEE, 2008.
- Lei Shi, Young-Rae Cho, Aidong Zhang, ”ANN Based Protein Function Prediction Using Integrated Protein-Protein Interaction Data”, International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, 2009.
- Benno Schwikowski, Peter Uetz, and Stanley Fields. ”A network of proteinprotein interactions in yeast”. In: Nature biotechnology 18.12 (2000), pp. 1257-1261.
- Guoxian Yu, Huzefa Rangwala, Carlotta Domeniconi, Guoji Zhang, and Zhiwen Yu, ”Protein Function Prediction with Incomplete Annotations”, IEEE/ACM Transactions On Computational Biology and Bioinformatics, Vol. 11, NO. 3, May/June 2014.
- Wei Peng, Min Li , Lu Chen, and Lusheng Wang, ”Predicting Protein Functions by Using Unbalanced Random Walk Algorithm on Three Biological Networks”, IEEE/ACM Transactions On Computational Biology and Bioinformatics, Vol. 14, NO. 2, March/April 2017.
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