M. Sultana, K. Kabir
· Chaos, Solitons & Fracta... · 0 citations
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Chaofeng Lan, Zhijun Tian, Chuang Han et al.
· Ocean Engineering · 0 citations
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Current structure-based drug design generative models often struggle to faithfully recapitulate genuine ligand-protein binding interactions. Instead, under the coupling of implicit learning architectures and biased training data, they tend to learn spurious statistical correlations. To address this, we propose EIP-Diff (Explicit Interaction-Prompted Diffusion), an architecture featuring a novel explicit interaction-prompt embedding mechanism that is better suited for real-world target-specific drug design. This architecture replaces biased implicit learning with explicit, residue-level biological guidance, thereby promoting more fine-grained geometric fidelity and more precise interaction-aware conditioning. To fully realize the capabilities of EIP-Diff and provide a reliable basis for performance evaluation, we further constructed CrystalData set, which provides higher-fidelity and less-biased structural supervision than existing data sets. This explicit architecture markedly improves distribution consistency: even when trained on the crossdocked data set, EIP-Diff achieves the highest alignment with authentic pharmacological distributions among evaluated models. Training on CrystalData set further enhances this alignment and improves 3D geometric accuracy, while retaining strong controllability, high chemical space coverage, and near-perfect uniqueness. In addition, target-based validation on KAT6A and YTHDC1 confirmed that EIP-Diff accurately recapitulates native-like binding modes. Furthermore, in a real-world drug design task against IDO1, we successfully designed a novel lead compound with nanomolar potency (IC50 = 0.31 nM). These results demonstrate that the EIP-Diff architecture can explicitly leverage experimentally derived structural data and biologically meaningful interaction information for target-specific molecular generation, thereby enabling its effective application to real-world structure-based drug design.
Huabin Du, Mingyang Wang, M. Luo et al.
· Journal of the American Chem... · 0 citations
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S. Marthi, M. Jha, D. Theilliol et al.
· Engineering applications of... · 0 citations
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Hao Zhang, Liangsheng Shi, Junzhe Cai et al.
· Journal of Water Process Eng... · 0 citations
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Mingqian Tang, Chunhui Yu, Can Li et al.
· Transportation Research Part... · 0 citations
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Omar Zeb, Iftikhar Ahmad, Sohail Iqbal
· Engineering applications of... · 0 citations
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Xiuxian Yin, Haoyu Yang, Weiwei Wu et al.
· Neurocomputing · 0 citations
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Zhucheng Liu, Feisheng Yang, Zhenyu Gong et al.
· Engineering applications of... · 0 citations
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Duo Yang, Xugan Liu, Yuefeng Liao et al.
· Engineering applications of... · 0 citations
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DRL is highlighted as a promising data-driven strategy for robust and adaptive control of nonlinear structural systems under partial observability by addressing a critical limitation of passive systems and accelerates the decay of residual vibrations.
Takehiko Asai
· Journal of Structural Engine... · 0 citations
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A. Leonidov, A. Titov, E. Vasilyeva
· Chaos, Solitons & Fracta... · 0 citations
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