CoCoPRED: coiled-coil protein structural feature prediction from amino acid sequence using deep neural networks
Abstract Motivation Coiled-coil is composed of two or more helices that are wound around each other. It widely exists in proteins and has been discovered to play a variety of critical roles in biology processes. Generally, there are three types of structural features in coiled-coil: coiled-coil doma...
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Veröffentlicht in: | Bioinformatics (Oxford, England) England), 2022-01, Vol.38 (3), p.720-729 |
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Zusammenfassung: | Abstract
Motivation
Coiled-coil is composed of two or more helices that are wound around each other. It widely exists in proteins and has been discovered to play a variety of critical roles in biology processes. Generally, there are three types of structural features in coiled-coil: coiled-coil domain (CCD), oligomeric state and register. However, most of the existing computational tools only focus on one of them.
Results
Here, we describe a new deep learning model, CoCoPRED, which is based on convolutional layers, bidirectional long short-term memory, and attention mechanism. It has three networks, i.e. CCD network, oligomeric state network, and register network, corresponding to the three types of structural features in coiled-coil. This means CoCoPRED has the ability of fulfilling comprehensive prediction for coiled-coil proteins. Through the 5-fold cross-validation experiment, we demonstrate that CoCoPRED can achieve better performance than the state-of-the-art models on both CCD prediction and oligomeric state prediction. Further analysis suggests the CCD prediction may be a performance indicator of the oligomeric state prediction in CoCoPRED. The attention heads in CoCoPRED indicate that registers a, b and e are more crucial for the oligomeric state prediction.
Availability and implementation
CoCoPRED is available at http://www.csbio.sjtu.edu.cn/bioinf/CoCoPRED. The datasets used in this research can also be downloaded from the website.
Supplementary information
Supplementary data are available at Bioinformatics online. |
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ISSN: | 1367-4803 1367-4811 |
DOI: | 10.1093/bioinformatics/btab744 |