Submit Manuscript  

Article Details


Protein Secondary Structure Prediction using Character n-gram Embedding and Bi-LSTM

Author(s):

Ashish Kumar Sharma* and Rajeev Srivastava   Pages 1 - 6 ( 6 )

Abstract:


Background: Protein secondary structure is vital to predicting the tertiary structure, which is essential in deciding protein function and drug designing. Therefore, there is a high requirement of computational methods to predict secondary structure from their primary sequence. Protein primary sequences represented as a linear combination of twenty amino acid characters and contain the contextual information for secondary structure prediction.

Objective and Methods: Protein secondary structure predicted from their primary sequences using a deep recurrent neural network. Protein secondary structure depends on local and long-range residues in primary sequences. In the proposed work, the local contextual information of amino acid residues captures with character n-gram. A dense embedding vector represents this local contextual information. Further, the bidirectional long short-term memory (Bi-LSTM) model is used to capture the long-range contexts by extracting the past and future residues information in primary sequences.

Results: The proposed deep recurrent architecture is evaluated for its efficacy for datasets namely ss.txt, RS126, and CASP9. The model shows the Q3 accuracies of 88.45%, 83.48%, and 86.69% for ss.txt, RS126, and CASP9, respectively. The performance of the proposed model is also compared with other state-of-the-art methods available in literature.

Conclusion: After a comparative analysis, it was observed that the proposed model is performing better in comparison to state-of-arts methods.

Keywords:

Proteomics, Protein Secondary Structure, Amino Acids Sequence, Character N-gram Embedding, Deep Learning, Bidirectional Long Short-Term Memory.

Affiliation:

Department of Computer Science and Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, Department of Computer Science and Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh



Read Full-Text article