RNAfcg: RNA Flexibility Prediction Based on Topological Centrality and Global Features.
Journal:
Journal of chemical information and modeling
Published Date:
Sep 14, 2024
Abstract
The dynamics of RNAs are related intimately to their functions. Molecular flexibility, as a starting point for understanding their dynamics, has been utilized to predict many characteristics associated with their functions. Since the experimental measurement methods are time-consuming and labor-intensive, it is urgently needed to develop reliable theoretical methods to predict RNA flexibility. In this work, we develop an effective machine learning method, RNAfcg, to predict RNA flexibility, where the Random Forest (RF) is trained by features including the topological centralities, flexibility-rigidity index, and global characteristics first introduced by us, as well as some traditional sequence and structural features. The analyses show that the three types of features introduced first have significant contributions to RNA flexibility prediction, among which the topological type contributes the most, which indicates the importance of structural topology in determining RNA flexibility. The performance comparison indicates that RNAfcg outperforms the state-of-the-art machine learning methods and the commonly used Gaussian Network Model (GNM) models, achieving a much higher Pearson correlation coefficient (PCC) of 0.6619 on the test data set. This work is helpful for understanding RNA dynamics and can be used to predict RNA function information. The source code is available at https://github.com/ChunhuaLab/RNAfcg/.