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<p>Identifying DNA binding sites remains a critical task in bioinformatics, with applications ranging from gene regulation studies to drug design. Although progress has been made in computational techniques, we still face challenges such as data complexity and prediction accuracy. In this paper, we introduce OptimDase, a new algorithm. It integrates feature encoding with optimum decision-making frameworks to improve DNA binding site prediction. OptimDase integrates multi-scale scanning and feature selection strategies, making it highly effective for both classification and regression tasks. Our experiments demonstrate that OptimDase achieves superior performance with an accuracy of 0.8943 in classification tasks and an RMSE of 0.0054 in regression tasks, outperforming existing algorithms in key evaluation metrics. These results highlight OptimDase’s portability and robustness, making it an effective solution for identifying DNA binding sites and advancing the applications of drug design.</p> Graphical Abstract <p></p>

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OptimDase: An Algorithm for Predicting DNA Binding Sites with Combined Feature Encoding

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年6月10日

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  • Zhendong Liu,
  • Jun S. Liu,
  • Dongqing Wei,
  • Rongjun Man,
  • Jiamin Jiang,
  • Bofeng Zhang,
  • Liping Li,
  • Zhiyong Zhao

摘要

Identifying DNA binding sites remains a critical task in bioinformatics, with applications ranging from gene regulation studies to drug design. Although progress has been made in computational techniques, we still face challenges such as data complexity and prediction accuracy. In this paper, we introduce OptimDase, a new algorithm. It integrates feature encoding with optimum decision-making frameworks to improve DNA binding site prediction. OptimDase integrates multi-scale scanning and feature selection strategies, making it highly effective for both classification and regression tasks. Our experiments demonstrate that OptimDase achieves superior performance with an accuracy of 0.8943 in classification tasks and an RMSE of 0.0054 in regression tasks, outperforming existing algorithms in key evaluation metrics. These results highlight OptimDase’s portability and robustness, making it an effective solution for identifying DNA binding sites and advancing the applications of drug design.

Graphical Abstract