Characterization and Prediction of Protein Flexibility Based on Structural Alphabets
Joint Authors
Liu, Bin
Dong, Qiwen
Wang, Kai
Liu, Xuan
Source
Issue
Vol. 2016, Issue 2016 (31 Dec. 2016), pp.1-7, 7 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2016-08-30
Country of Publication
Egypt
No. of Pages
7
Main Subjects
Abstract EN
Motivation.
To assist efforts in determining and exploring the functional properties of proteins, it is desirable to characterize and predict protein flexibilities.
Results.
In this study, the conformational entropy is used as an indicator of the protein flexibility.
We first explore whether the conformational change can capture the protein flexibility.
The well-defined decoy structures are converted into one-dimensional series of letters from a structural alphabet.
Four different structure alphabets, including the secondary structure in 3-class and 8-class, the PB structure alphabet (16-letter), and the DW structure alphabet (28-letter), are investigated.
The conformational entropy is then calculated from the structure alphabet letters.
Some of the proteins show high correlation between the conformation entropy and the protein flexibility.
We then predict the protein flexibility from basic amino acid sequence.
The local structures are predicted by the dual-layer model and the conformational entropy of the predicted class distribution is then calculated.
The results show that the conformational entropy is a good indicator of the protein flexibility, but false positives remain a problem.
The DW structure alphabet performs the best, which means that more subtle local structures can be captured by large number of structure alphabet letters.
Overall this study provides a simple and efficient method for the characterization and prediction of the protein flexibility.
American Psychological Association (APA)
Dong, Qiwen& Wang, Kai& Liu, Bin& Liu, Xuan. 2016. Characterization and Prediction of Protein Flexibility Based on Structural Alphabets. BioMed Research International،Vol. 2016, no. 2016, pp.1-7.
https://search.emarefa.net/detail/BIM-1097829
Modern Language Association (MLA)
Dong, Qiwen…[et al.]. Characterization and Prediction of Protein Flexibility Based on Structural Alphabets. BioMed Research International No. 2016 (2016), pp.1-7.
https://search.emarefa.net/detail/BIM-1097829
American Medical Association (AMA)
Dong, Qiwen& Wang, Kai& Liu, Bin& Liu, Xuan. Characterization and Prediction of Protein Flexibility Based on Structural Alphabets. BioMed Research International. 2016. Vol. 2016, no. 2016, pp.1-7.
https://search.emarefa.net/detail/BIM-1097829
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1097829