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    HyPepTox-Fuse: An interpretable hybrid framework for accurate peptide toxicity prediction fusing protein language model-based embeddings with conventional descriptors by Duong Thanh Tran, Nhat Truong Pham, Nguyen Doan Hieu Nguyen, Leyi Wei, Balachandran Manavalan

    Published 2025-08-01
    “…Moreover, we conducted a case study to validate the robustness and generalizability of HyPepTox-Fuse, highlighting its effectiveness in enhancing model performance. Furthermore, the HyPepTox-Fuse server is freely accessible at https://balalab-skku.org/HyPepTox-Fuse/ and the source code is publicly available at https://github.com/cbbl-skku-org/HyPepTox-Fuse/. …”
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    Learning motif features and topological structure of molecules for metabolic pathway prediction by Jianguo Hu, Yiqing Zhang, Jinxin Xie, Zhen Yuan, Zhangxiang Yin, Shanshan Shi, Honglin Li, Shiliang Li

    Published 2025-04-01
    “…MotifMol3D is an open-source tool that is available at https://github.com/Irena-Zhang/MotifMol3D.git . Scientific contribution MotifMol3D integrates motif information, graph neural networks, and 3D structural data to enhance feature extraction for small-sample molecules, improving the precision and interpretability of metabolic pathway predictions. …”
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