Classifying the molecular functions of Rab GTPases in membrane trafficking using deep convolutional neural networks

Nguyen Quoc Khanh Le, Quang Thai Ho, Yu Yen Ou

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

Deep learning has been increasingly used to solve a number of problems with state-of-the-art performance in a wide variety of fields. In biology, deep learning can be applied to reduce feature extraction time and achieve high levels of performance. In our present work, we apply deep learning via two-dimensional convolutional neural networks and position-specific scoring matrices to classify Rab protein molecules, which are main regulators in membrane trafficking for transferring proteins and other macromolecules throughout the cell. The functional loss of specific Rab molecular functions has been implicated in a variety of human diseases, e.g., choroideremia, intellectual disabilities, cancer. Therefore, creating a precise model for classifying Rabs is crucial in helping biologists understand the molecular functions of Rabs and design drug targets according to such specific human disease information. We constructed a robust deep neural network for classifying Rabs that achieved an accuracy of 99%, 99.5%, 96.3%, and 97.6% for each of four specific molecular functions. Our approach demonstrates superior performance to traditional artificial neural networks. Therefore, from our proposed study, we provide both an effective tool for classifying Rab proteins and a basis for further research that can improve the performance of biological modeling using deep neural networks.

Original languageEnglish
Pages (from-to)33-41
Number of pages9
JournalAnalytical Biochemistry
Volume555
DOIs
Publication statusPublished - Aug 15 2018
Externally publishedYes

Fingerprint

rab GTP-Binding Proteins
Learning
Neural networks
Membranes
Choroideremia
Position-Specific Scoring Matrices
Proteins
Drug Design
Protein Transport
Macromolecules
Intellectual Disability
Feature extraction
Molecules
Research
Pharmaceutical Preparations
Deep learning
Neoplasms
Deep neural networks

Keywords

  • Classification
  • Deep learning
  • DeepRab
  • Membrane trafficking
  • Neural networks
  • Rab protein

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Classifying the molecular functions of Rab GTPases in membrane trafficking using deep convolutional neural networks. / Le, Nguyen Quoc Khanh; Ho, Quang Thai; Ou, Yu Yen.

In: Analytical Biochemistry, Vol. 555, 15.08.2018, p. 33-41.

Research output: Contribution to journalArticle

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