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Sheng-Wen Yang

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#graph neural networks Open access Oct 2026

Tractable and Thermodynamically Consistent pKa Prediction via First-Dissociation Aggregation

Ionization governs molecular behavior, yet predicting aqueous pKa accurately and tractably remains a fundamental challenge. Rigorous ensemble methods require enumerating a protonation-state space that grows exponentially with the number of ionizable sites, while fast graph predictors return numbers without thermodynami...

Zhuo-Yan Liu, Qiu-Yin Zhu, Qing-Kun Li et al. · 0 citations
Open access Oct 2026

Beyond RMSD: Deterministic Dlow Matching for Ultrafast and Physically Validated Transition-State Generation

Transition state (TS) generation is typically evaluated by geometric similarity, yet low root-mean-square deviation (RMSD) does not establish first-order saddle-point character or reaction-path connectivity. Here we introduce Kairos-GFM, a deterministic equivariant flow-matching model that combines a two-dimensional re...

He-Hua Li, Sai-Sai Yu, Qiu-Yin Zhu et al. · 0 citations

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