P3CMQA: Single-Model Quality Assessment Using 3DCNN with Profile-Based Features

2021

Bioengineering, Vol 8, Iss 3, p 40 (2021)

Model quality assessment (MQA), which selects near-native structures from structure models, is an important process in protein tertiary structure prediction. The three-dimensional convolution neural network (3DCNN) was applied to the task, but the performance was comparable to existing methods because it used only atom-type features as the input. Thus, we added sequence profile-based features, which are also used in other methods, to improve the performance. We developed a single-model MQA method for protein structures based on 3DCNN using sequence profile-based features, namely, P3CMQA. Performance evaluation using a CASP13 dataset showed that profile-based features improved the assessment performance, and the proposed method was better than currently available single-model MQA methods, including the previous 3DCNN-based method. We also implemented a web-interface of the method to make it more user-friendly.

article

English

MDPI AG, 2021.

model quality assessment (MQA), estimation of model accuracy (EMA), protein structure prediction, machine learning, deep learning, 3DCNN, Technology, Biology (General), QH301-705.5