PreDBA: A heterogeneous ensemble approach for predicting protein-DNA binding affinity

Abstract

The interaction between protein and DNA plays an essential function in various critical natural processes, like DNA replication, transcription, splicing, and repair. Studying the binding affinity of proteins to DNA helps to understand the recognition mechanism of protein-DNA complexes. Since there are still many limitations on the protein-DNA binding affinity data measured by experiments, accurate and reliable calculation methods are necessarily required. So we put forward a computational approach in this paper, called PreDBA, that can forecast protein-DNA binding affinity effectively by using heterogeneous ensemble models. One hundred protein-DNA complexes are manually collected from the related literature as a data set for protein-DNA binding affinity. Then, 52 sequence and structural features are obtained. Based on this, the correlation between these 52 characteristics and protein-DNA binding affinity is calculated. Furthermore, we found that the protein-DNA binding affinity is affected by the DNA molecule structure of the compound. We classify all protein-DNA compounds into five classifications based on the DNA structure related to the proteins that make up the protein-DNA complexes. In each group, a stacked heterogeneous ensemble model is constructed based on the obtained features. In the end, based on the binding affinity data set, we used the leave-one-out cross-validation to evaluate the proposed method comprehensively. In the five categories, the Pearson correlation coefficient values of our recommended method range from 0.735 to 0.926. We have demonstrated the advantages of the proposed method compared to other machine learning methods and currently existing protein-DNA binding affinity prediction approach.

Web tools support predicting protein–nucleic acid complexes stability with affinity changes

“…An affinity dataset was constructed by manually collecting 100 nonredundant protein-DNA complexes. These web servers predict protein-RNA/DNA binding affinity well (Yang & Deng, 2020). However, developing a web server that can freely predict protein-nucleic acid binding affinity would be more user-friendly for researchers.…”

Host-pathogen protein-nucleic acid interactions: A comprehensive review

“…DNA binding specificity arises from all of the above. The shape is also a key factor, and recently a database that annotated transcription factor binding sites based on shape was described [334] . Algorithms for RNA binding sites have also been constructed [335] .…”

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