Deep Learning Approaches for Protein Structure Prediction

  • Authors

    • Khatri Chandni
    • Prof. Mrudang Pandya
    • Dr. Sunil Jardosh
    2018-09-22
    https://doi.org/10.14419/ijet.v7i4.5.20037
  • Bioinformatics, Protein Contact Mapping, Protein-Protein Interactions, Protein Structure Prediction, Protein Docking, Protein Folding, DeepLearning
  • Abstract

    In recent years, Machine Learning techniques that are based on Deep Learning networks that show a great promise in research          communities.Successful methods for deep learning involve Artificial Neural Networks and Machine Learning. Deep Learning solves severa  problems in bioinformatics. Protein Structure Prediction is one of the most important fields that can be solving using Deep Learning  approaches.These protein are categorized on basis of occurrence of amino acid patterns occur to extract the feature. In these paper aimed to review work based on protein structure prediction solve using Deep Learning Networks. Objective is to review motivate and facilitatethese deep learn the network for predicting protein sequences using Deep Learning.

     

  • References

    1. [1] Matt Spencer, Jesse Eickholt, and Jianlin Cheng; A DeepLearning Network Approach to ab initio Protein Secondary Structure Predictio IEEE/ACM Trans Comput Biol Bioinform. 2015 Jan-Feb; 12(1): 103–112. Published online2014 Aug 7. doi: 10.1109/TCBB.2014.2343960.

      [2] Floudas C, Fung H, McAllister S, Mönnigmann M, Rajgaria R. Advances in protein structure prediction and de novo protein design: A review. Chemical EngineeringScience.2006;61:966–988.

      [3] Kopp J, Schwede T. Automated protein structure homologymodeling: a progress report. Pharmacogenomics. 2004;5:405–416

      [4] Hinton GE, Osindero S, Teh Y-W. A fast learning algorithmfor deep belief nets. Neural computation. 2006;18:1527–1554.

      [5] Arel I et al. Deep Machine Learning- A New Frontier in Artificial Intelligence Research. IEEE Computational Intelligence 2010; 13- 18

      [6] J. Schmidhuber., "My First Deep Learning System of 1991 +Deep Learning Timeline 1962–2013.".

      [7] Song, H.A.; Lee, S. Y. (2013). "Hierarchical Representation Using NMF". Neural Information Processing. Lectures Notes in Computer Sciences 8226. Springer Berlin Heidelberg. pp. 466– 473.doi:10.1007/978-3-642-42054- 2_58. ISBN 978-3-642-42053- 5.Cadence, “Encounter user guide,†Version 6.2.4, March 2008.

      [8] J. Schmidhuber., "Learning complex, extended sequences using the principle of history compression," Neural Computation, 4, pp. 234– 242, 1992.

      [9] Busia, Akosua & Jaitly, Navdeep “Next-Step Conditioned Deep Convolutional Neural Networks Improve Protein Secondary Structure Prediction†arXiv:1702.03865 2017 p1-11.

      [10] Jian Zhou and Olga G. Troyanskaya. Deep supervised and convolutional generative stochastic network for protein secondary structure prediction. Journal of Machine Learning Research: W&CP, 32(1):754-762, 2014.

      [11] Zeming Lin, Jack Lanchantin, and Yanjun Qi. 2016. MUST-CNN: a multilayer shift-and-stitch deep convolutional architecture for sequence-based protein structure prediction. In Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence (AAAI'16). AAAI Press 27-34.

      [12] Qi, Y.; Oja, M.;Weston, J.; and Noble,W. S. 2012. A unified multitask architecture for predicting local protein properties.PloS one7(3):e 3235.

      [13] Drozdetskiy, A.; Cole, C.; Procter, J.; and Barton, G. J. 2015.JPred4: a protein secondary structure prediction server. Nucleic Acids Research gkv332.

      [13]] James Lyons, Abdollah Dehzangi, Rhys Heffernan, Alok Sharma, Kuldip Paliwal, Abdul Sattar, Yaoqi Zhou, and Yuedong Yang. Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse autoencoder deep neural network. Journal of Computational Chemistry, 35(28):2040-2046, 2014.

      [14] Wang Z, Zhao F, Peng J, Xu J “Protein 8-class secondary structure prediction using conditional neural fields†Proteomics. 2011 Oct;11(19):3786-92. doi: 10.1002/pmic.201100196. Epub 2011 Aug 31.

      [15] Pietro Di Lena, Ken Nagata, and Pierre Baldi. Deepspatiotemporal architectures and learning for protein structure prediction. Advances in Neural Information Processing Systems (NIPS) 25, pages 521-529, Lake Tahoe, Nevada, December 3 – 6, 2012.

      [16] Pietro Di Lena, Ken Nagata, and Pierre Baldi. Deep architectures for protein contact map prediction. Bioinformatics, 28(19):2449- 2457, 2012.

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  • How to Cite

    Chandni, K., Mrudang Pandya, P., & Sunil Jardosh, D. (2018). Deep Learning Approaches for Protein Structure Prediction. International Journal of Engineering & Technology, 7(4.5), 168-170. https://doi.org/10.14419/ijet.v7i4.5.20037

    Received date: 2018-09-22

    Accepted date: 2018-09-22

    Published date: 2018-09-22