Improving Protein Gamma-Turn Prediction Using Inception Capsule Networks

Sci Rep. 2018 Oct 24;8(1):15741. doi: 10.1038/s41598-018-34114-2.

Abstract

Protein gamma-turn prediction is useful in protein function studies and experimental design. Several methods for gamma-turn prediction have been developed, but the results were unsatisfactory with Matthew correlation coefficients (MCC) around 0.2-0.4. Hence, it is worthwhile exploring new methods for the prediction. A cutting-edge deep neural network, named Capsule Network (CapsuleNet), provides a new opportunity for gamma-turn prediction. Even when the number of input samples is relatively small, the capsules from CapsuleNet are effective to extract high-level features for classification tasks. Here, we propose a deep inception capsule network for gamma-turn prediction. Its performance on the gamma-turn benchmark GT320 achieved an MCC of 0.45, which significantly outperformed the previous best method with an MCC of 0.38. This is the first gamma-turn prediction method utilizing deep neural networks. Also, to our knowledge, it is the first published bioinformatics application utilizing capsule network, which will provide a useful example for the community. Executable and source code can be download at http://dslsrv8.cs.missouri.edu/~cf797/MUFoldGammaTurn/download.html.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Computational Biology / methods
  • Neural Networks, Computer*
  • Protein Structure, Secondary*
  • Proteins / chemistry*

Substances

  • Proteins