Author

Yi-Jie Ding

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Open access Oct 2026

Pocket Contrastive Learning and Conformation Fusion for Robust Structure-Conditioned 3D Molecular Generation under Receptor Conformational Variation.

MOTIVATION Pocket-conditioned molecular generation incorporates the three-dimensional geometry and chemical environment of protein binding sites into molecular design. However, receptor conformational variation can introduce distribution shifts between training and inference, particularly under cross-docking conditions...

Huan Liu, Yi-Jie Ding, Xiao-Yi Guo et al. · Bioinformatics · 0 citations

Open access Sep 2026

AET5: A transcriptome-guided molecular generation framework with contrastive self-supervised learning

AET5 is presented, a de novo molecular generation framework that conditions molecular design on disease-reversal gene expression profiles, providing a general framework for biologically informed drug design under noisy transcriptomic conditions.

Zhi-Kang Yuan, Xin Zhang, Gao-Ming Lin et al. · PLoS Computational Biology · 0 citations

Aug 2026

MDFA-MLP: Multi-scale Dilated Fusion Attention and Ensemble Framework for Anticancer Peptide Prediction.

INTRODUCTION Experimental identification of anticancer peptides (ACPs) is timeconsuming and costly, which limits large-scale ACP discovery and screening. To address this challenge, we developed MDFA-MLP, a novel computational framework for ACP prediction that integrates multi-scale feature learning and ensemble classif...

Binyu Li, Zhi-Hua Huang, Yi-Jie Ding et al. · Combinatorial chemistry & hi... · 0 citations