Enhancing protein backbone angle prediction by using simpler models of deep neural networks

Loading...
Thumbnail Image
File version

Version of Record (VoR)

Author(s)
Mataeimoghadam, Fereshteh
Newton, MA Hakim
Dehzangi, Abdollah
Karim, Abdul
Jayaram, B
Ranganathan, Shoba
Sattar, Abdul
Griffith University Author(s)
Primary Supervisor
Other Supervisors
Editor(s)
Date
2020
Size
File type(s)
Location
Abstract

Protein structure prediction is a grand challenge. Prediction of protein structures via the representations using backbone dihedral angles has recently achieved significant progress along with the on-going surge of deep neural network (DNN) research in general. However, we observe that in the protein backbone angle prediction research, there is an overall trend to employ more and more complex neural networks and then to throw more and more features to the neural networks. While more features might add more predictive power to the neural network, we argue that redundant features could rather clutter the scenario and more complex neural networks then just could counterbalance the noise. From artificial intelligence and machine learning perspectives, problem representations and solution approaches do mutually interact and thus affect performance. We also argue that comparatively simpler predictors can more easily be reconstructed than the more complex ones. With these arguments in mind, we present a deep learning method named Simpler Angle Predictor (SAP) to train simpler DNN models that enhance protein backbone angle prediction. We then empirically show that SAP can significantly outperform existing state-of-the-art methods on well-known benchmark datasets: for some types of angles, the differences are 6–8 in terms of mean absolute error (MAE). The SAP program along with its data is available from the website https://gitlab.com/mahnewton/sap.

Journal Title

Scientific Reports

Conference Title
Book Title
Edition
Volume

10

Issue

1

Thesis Type
Degree Program
School
Publisher link
Patent number
Funder(s)
Grant identifier(s)
Rights Statement
Rights Statement

© The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.

Item Access Status
Note
Access the data
Related item(s)
Subject

Artificial intelligence

Science & Technology

Multidisciplinary Sciences

Science & Technology - Other Topics

SECONDARY STRUCTURE PREDICTION

REAL-VALUE PREDICTION

Persistent link to this record
Citation

Mataeimoghadam, F; Newton, MAH; Dehzangi, A; Karim, A; Jayaram, B; Ranganathan, S; Sattar, A, Enhancing protein backbone angle prediction by using simpler models of deep neural networks, Scientific Reports, 2020, 10 (1), pp. 19430

Collections