Prediction of Protein B-factor Profiles based on Bidirectional Long Short-Term Memory Network

14 September 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


B-factor is a measure of ray attenuation or scattering caused by atomic thermal motion during X-ray diffraction of protein crystal structure. B-factor reflects the vibration of atoms; hence, it is the most common experimental descriptor of protein flexibility and has been extensively applied in the studies of protein dynamics, screening of bioactive small molecules, and protein engineering. The prediction of B-factor profiles has considerable significance for analyzing the dynamic properties of unknown proteins. Deep learning technology has developed rapidly in recent years and has been widely implemented in many research fields, especially structural biology. In this paper, a deep neural network model based on bidirectional long short-term memory (biLSTM) network is proposed to predict the B-factor profile of a protein by combining its sequence-based features and structure-based features. Based on a large dataset of high-resolution proteins, our method predicts the B-factor profiles with an average Pearson correlation coefficient (PCC) of 0.71, and 85% of the B-factor profiles have a PCC greater than 0.6, which indicates a strong correlation between predicted and experimental values. In addition, our method remarkably outperforms the existing methods on four test datasets with different protein sizes.


B-factor profiles prediction
protein flexibility
bidirectional long short-term memory
deep learning


Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.