Xie W, Feng YE. Prediction of the Disordered Regions of Intrinsically Disordered Proteins Based on the Molecular Functions.
Protein Pept Lett 2020;
27:279-286. [PMID:
30819075 DOI:
10.2174/0929866526666190226160629]
[Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 01/03/2019] [Accepted: 02/08/2019] [Indexed: 01/29/2023]
Abstract
BACKGROUND
Intrinsically disordered proteins lack a well-defined three dimensional structure under physiological conditions while possessing the essential biological functions. They take part in various physiological processes such as signal transduction, transcription and posttranslational modifications and etc. The disordered regions are the main functional sites for intrinsically disordered proteins. Therefore, the research of the disordered regions has become a hot issue.
OBJECTIVE
In this paper, our motivation is to analysis of the features of disordered regions with different molecular functions and predict of different disordered regions using valid features.
METHODS
In this article, according to the different molecular function, we firstly divided intrinsically disordered proteins into six classes in DisProt database. Then, we extracted four features using bioinformatics methods, namely, Amino Acid Index (AAIndex), codon frequency (Codon), three kinds of protein secondary structure compositions (3PSS) and Chemical Shifts (CSs), and used these features to predict the disordered regions of the different functions by Support Vector Machine (SVM).
RESULTS
The best overall accuracy was 99.29% using the chemical shift (CSs) as feature. In feature fusion, the overall accuracy can reach 88.70% by using CSs+AAIndex as features. The overall accuracy was up to 86.09% by using CSs+AAIndex+Codon+3PSS as features.
CONCLUSION
We predicted and analyzed the disordered regions based on the molecular functions. The results showed that the prediction performance can be improved by adding chemical shifts and AAIndex as features, especially chemical shifts. Moreover, the chemical shift was the most effective feature in the prediction. We hoped that our results will be constructive for the study of intrinsically disordered proteins.
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