CWFBind: Geometry-Awareness for Fast and Accurate Protein-Ligand Docking
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arXiv
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| Autores principales: | , , |
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| Formato: | Preprint |
| Publicado: |
2025
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| _version_ | 1866915443802898432 |
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| author | Jia, Liyan Ren, Chuan-Xian Yan, Hong |
| author_facet | Jia, Liyan Ren, Chuan-Xian Yan, Hong |
| contents | Accurately predicting the binding conformation of small-molecule ligands to protein targets is a critical step in rational drug design. Although recent deep learning-based docking surpasses traditional methods in speed and accuracy, many approaches rely on graph representations and language model-inspired encoders while neglecting critical geometric information, resulting in inaccurate pocket localization and unrealistic binding conformations. In this study, we introduce CWFBind, a weighted, fast, and accurate docking method based on local curvature features. Specifically, we integrate local curvature descriptors during the feature extraction phase to enrich the geometric representation of both proteins and ligands, complementing existing chemical, sequence, and structural features. Furthermore, we embed degree-aware weighting mechanisms into the message passing process, enhancing the model's ability to capture spatial structural distinctions and interaction strengths. To address the class imbalance challenge in pocket prediction, CWFBind employs a ligand-aware dynamic radius strategy alongside an enhanced loss function, facilitating more precise identification of binding regions and key residues. Comprehensive experimental evaluations demonstrate that CWFBind achieves competitive performance across multiple docking benchmarks, offering a balanced trade-off between accuracy and efficiency. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2508_09499 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | CWFBind: Geometry-Awareness for Fast and Accurate Protein-Ligand Docking Jia, Liyan Ren, Chuan-Xian Yan, Hong Computer Vision and Pattern Recognition Computational Geometry Machine Learning Accurately predicting the binding conformation of small-molecule ligands to protein targets is a critical step in rational drug design. Although recent deep learning-based docking surpasses traditional methods in speed and accuracy, many approaches rely on graph representations and language model-inspired encoders while neglecting critical geometric information, resulting in inaccurate pocket localization and unrealistic binding conformations. In this study, we introduce CWFBind, a weighted, fast, and accurate docking method based on local curvature features. Specifically, we integrate local curvature descriptors during the feature extraction phase to enrich the geometric representation of both proteins and ligands, complementing existing chemical, sequence, and structural features. Furthermore, we embed degree-aware weighting mechanisms into the message passing process, enhancing the model's ability to capture spatial structural distinctions and interaction strengths. To address the class imbalance challenge in pocket prediction, CWFBind employs a ligand-aware dynamic radius strategy alongside an enhanced loss function, facilitating more precise identification of binding regions and key residues. Comprehensive experimental evaluations demonstrate that CWFBind achieves competitive performance across multiple docking benchmarks, offering a balanced trade-off between accuracy and efficiency. |
| title | CWFBind: Geometry-Awareness for Fast and Accurate Protein-Ligand Docking |
| topic | Computer Vision and Pattern Recognition Computational Geometry Machine Learning |
| url | https://arxiv.org/abs/2508.09499 |