ResCap-DBP: A Lightweight Residual-Capsule Network for Accurate DNA-Binding Protein Prediction Using Global ProteinBERT Embeddings

TL;DR

This paper introduces ResCap-DBP, a deep learning model combining residual encoders and capsule networks with ProteinBERT embeddings to accurately predict DNA-binding proteins from sequences, outperforming existing methods.

Contribution

The study presents a novel deep learning framework that effectively integrates global protein embeddings with advanced neural architectures for improved DNA-binding protein prediction.

Findings

ProteinBERT embeddings outperform traditional encodings on large datasets.

ResCap-DBP achieves high AUC scores, e.g., 98.0% on PDB14189.

Model maintains balanced sensitivity and specificity across datasets.

Abstract

DNA-binding proteins (DBPs) are integral to gene regulation and cellular processes, making their accurate identification essential for understanding biological functions and disease mechanisms. Experimental methods for DBP identification are time-consuming and costly, driving the need for efficient computational prediction techniques. In this study, we propose a novel deep learning framework, ResCap-DBP, that combines a residual learning-based encoder with a one-dimensional Capsule Network (1D-CapsNet) to predict DBPs directly from raw protein sequences. Our architecture incorporates dilated convolutions within residual blocks to mitigate vanishing gradient issues and extract rich sequence features, while capsule layers with dynamic routing capture hierarchical and spatial relationships within the learned feature space. We conducted comprehensive ablation studies comparing global and local embeddings from ProteinBERT and conventional one-hot encoding. Results show that ProteinBERT embeddings substantially outperform other representations on large datasets. Although one-hot encoding showed marginal advantages on smaller datasets, such as PDB186, it struggled to scale effectively. Extensive evaluations on four pairs of publicly available benchmark datasets demonstrate that our model consistently outperforms current state-of-the-art methods. It achieved AUC scores of 98.0% and 89.5% on PDB14189andPDB1075, respectively. On independent test sets PDB2272 and PDB186, the model attained top AUCs of 83.2% and 83.3%, while maintaining competitive performance on larger datasets such as PDB20000. Notably, the model maintains a well balanced sensitivity and specificity across datasets. These results demonstrate the efficacy and generalizability of integrating global protein representations with advanced deep learning architectures for reliable and scalable DBP prediction in diverse genomic contexts.