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IMPContact: An Interhelical Residue Contact Prediction Method
Joint Authors
Wang, Han
Hu, LiHong
Lu, Ying Hua
Fang, Chao
Jia, Yajie
Source
Issue
Vol. 2020, Issue 2020 (31 Dec. 2020), pp.1-10, 10 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2020-03-27
Country of Publication
Egypt
No. of Pages
10
Main Subjects
Abstract EN
As an important category of proteins, alpha-helix transmembrane proteins (αTMPs) play an important role in various biological activities.
Because the solved αTMP structures are inadequate, predicting the residue contacts among the transmembrane segments of an αTMP exhibits the basis of protein fold, which can be used to further discover more protein functions.
A few efforts have been devoted to predict the interhelical residue contact using machine learning methods based on the prior knowledge of transmembrane protein structure.
However, it is still a challenge to improve the prediction accuracy, while the deep learning method provides an opportunity to utilize the structural knowledge in a different insight.
For this purpose, we proposed a novel αTMP residue-residue contact prediction method IMPContact, in which a convolutional neural network (CNN) was applied to recognize those interhelical contacts in a TMP using its specific structural features.
There were four sequence-based TMP-specific features selected to descript a pair of residues, namely, evolutionary covariation, predicted topology structure, residue relative position, and evolutionary conservation.
An up-to-date dataset was used to train and test the IMPContact; our method achieved better performance compared to peer methods.
In the case studies, IHRCs in the regular transmembrane helixes were better predicted than in the irregular ones.
American Psychological Association (APA)
Fang, Chao& Jia, Yajie& Hu, LiHong& Lu, Ying Hua& Wang, Han. 2020. IMPContact: An Interhelical Residue Contact Prediction Method. BioMed Research International،Vol. 2020, no. 2020, pp.1-10.
https://search.emarefa.net/detail/BIM-1133997
Modern Language Association (MLA)
Fang, Chao…[et al.]. IMPContact: An Interhelical Residue Contact Prediction Method. BioMed Research International No. 2020 (2020), pp.1-10.
https://search.emarefa.net/detail/BIM-1133997
American Medical Association (AMA)
Fang, Chao& Jia, Yajie& Hu, LiHong& Lu, Ying Hua& Wang, Han. IMPContact: An Interhelical Residue Contact Prediction Method. BioMed Research International. 2020. Vol. 2020, no. 2020, pp.1-10.
https://search.emarefa.net/detail/BIM-1133997
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1133997