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Author

Zhen-Ling Peng

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Open access Oct 2026

trFlow: ultrafast all-atom protein conformational ensemble generation via conditional flow matching

Generating diverse, all-atom protein conformations remains challenging, especially for recovering alternative functional states and modeling conformational ensembles. We present trFlow, an ultrafast approach for generating all-atom conformations using geometry-guided flow matching. trFlow leverages three core innovatio...

Chen-Xiao Xiang, Kai-Long Zhao, Zhen-Ling Peng et al. · 0 citations
Aug 2026

UniPoseScore: A Unified Graphormer3D-Based Framework for Protein-Ligand Binding Pose Scoring and Refinement.

UniPoseScore, a Graphormer3D-based framework for ligand pose scoring and refinement, simultaneously predicts pose RMSD and atomic displacement vectors to guide ligand pose refinement and suggests that the model captures structural features correlated with pose accuracy.

Jin-Qiao Zhang, Xin-Yu Ren, Zhen-Ling Peng et al. · 0 citations
Open access Jul 2026

COACH-D 2.0: A Server for Template-based Modeling of Protein-ligand Interactions.

COACH-D 2.0 is introduced, a substantially enhanced template-based method for predicting protein-ligand binding sites and features three key advances: integration of multimeric templates from Q-BioLiP into the authors' in-house library, a new multimeric structure processing module enabling binding site prediction for p...

Xiao-Yu An, Hong Wei, Wenkai Wang et al. · 0 citations

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