AlphaCutter: Efficient removal of non-globular regions from predicted protein structures

A huge number of high-quality predicted protein structures are now publicly available. However, many of these structures contain non-globular regions, which diminish the performance of downstream structural bioinformatic applications. In this study, we develop AlphaCutter for the removal of non-globular regions from predicted protein structures. A large-scale cleaning of 542,380 predicted SwissProt structures highlights that AlphaCutter is able to (1) remove non-globular regions that are undetectable using pLDDT scores and (2) preserve high integrity of the cleaned domain regions. As useful applications, AlphaCutter improved the folding energy scores and sequence recovery rates in the re-design of domain regions. On average, AlphaCutter takes less than 3 s to clean a protein structure, enabling efficient cleaning of the exploding number of predicted protein structures. AlphaCutter is available at https://github.com/johnnytam100/AlphaCutter . AlphaCutter-cleaned SwissProt structures are available for download at https://doi.org/10.5281/zenodo.7944483 .     

Multiple characteristics analysis of Alzheimer’s electroencephalogram by power spectral density and Lempel–Ziv complexity

To investigate the electroencephalograph (EEG) background activity in patients with Alzheimer’s disease (AD), power spectrum density (PSD) and Lempel–Ziv (LZ) complexity analysis are proposed to extract multiple effective features of EEG signals from AD patients and further applied to distinguish AD patients from the normal controls. Spectral analysis based on autoregressive Burg method is first used to quantify the power distribution of EEG series in the frequency domain. Compared with the control group, the relative PSD of AD group is significantly higher in the theta frequency band while lower in the alpha frequency bands. In order to explore the nonlinear information, Lempel–Ziv complexity (LZC) and multi-scale LZC is further applied to all electrodes for the four frequency bands. Analysis results demonstrate that the group difference is significant in the alpha frequency band by LZC and multi-scale LZC analysis. However, the group difference of multi-scale LZC is much more remarkable, manifesting as more channels undergo notable changes, particularly in electrodes O1 and O2 in the occipital area. Moreover, the multi-scale LZC value provided a better classification between the two groups with an accuracy of 85.7 %. In addition, we combine both features of the relative PSD and multi-scale LZC to discriminate AD patients from the normal controls by applying a support vector machine model in the alpha frequency band. It is indicated that the two groups can be clearly classified by the combined feature. Importantly, the accuracy of the classification is higher than that of any one feature, reaching 91.4 %. The obtained results show that analysis of PSD and multi-scale LZC can be taken as a potential comprehensive measure to distinguish AD patients from the normal controls, which may benefit our understanding of the disease.