Predicting protein-peptide binding residues via interpretable deep learning. - Ruheng Wang; Junru Jin; Quan Zou 001; Kenta Nakai; Leyi Wei (Bioinform., 2022)

Multi-view deep learning based molecule design and structural optimization accelerates the SARS-CoV-2 inhibitor discovery. - Chao Pang; Yu Wang; Yi Jiang; Ruheng Wang; Ran Su; Leyi Wei (CoRR, 2022)

ConPep: Prediction of peptide contact maps with pre-trained biological language model and multi-view feature extracting strategy. - Qingxin Wei; Ruheng Wang; Yi Jiang; Leyi Wei; Yu Sun; Jie Geng; Ran Su (Comput. Biol. Medicine, 2023)

An interpretable deep learning model predicts RNA-small molecule binding sites. - Wen-Yu Xi; Ruheng Wang; Li Wang; Xiucai Ye; Mingyang Liu; Tetsuya Sakurai (Future Gener. Comput. Syst., 2024)

AttenSyn: An Attention-Based Deep Graph Neural Network for Anticancer Synergistic Drug Combination Prediction. - Tianshuo Wang; Ruheng Wang; Leyi Wei (J. Chem. Inf. Model., 2024)

CACPP: A Contrastive Learning-Based Siamese Network to Identify Anticancer Peptides Based on Sequence Only. - Xuetong Yang; Junru Jin; Ruheng Wang; Zhongshen Li; Yu Wang; Leyi Wei (J. Chem. Inf. Model., 2024)

MucLiPred: Multi-Level Contrastive Learning for Predicting Nucleic Acid Binding Residues of Proteins. - Jiashuo Zhang 002; Ruheng Wang; Leyi Wei (J. Chem. Inf. Model., 2024)

Multi-CGAN: Deep Generative Model-Based Multiproperty Antimicrobial Peptide Design. - Haoqing Yu; Ruheng Wang; Jianbo Qiao; Leyi Wei (J. Chem. Inf. Model., 2024)

NanoCon: contrastive learning-based deep hybrid network for nanopore methylation detection. - Chenglin Yin; Ruheng Wang; Jianbo Qiao; Hua Shi; Hongliang Duan; Xinbo Jiang; Saisai Teng; Leyi Wei (Bioinform., 2024)

PepThink-R1: LLM for Interpretable Cyclic Peptide Optimization with CoT SFT and Reinforcement Learning. - Ruheng Wang; Hang Zhang; Trieu Nguyen; Shasha Feng; Hao-Wei Pang; Xiang Yu; Li Xiao; Peter Zhiping Zhang (CoRR, 2025)

Multiview Deep Learning-Based Molecule Design and Structural Optimization Accelerates Inhibitor Discover. - Chao Pang; Yu Wang; Yi Jiang; Ruheng Wang; Xiaojun Yao; Quan Zou 001; Xiangxiang Zeng; Ran Su; Leyi Wei (IEEE Trans. Neural Networks Learn. Syst., 2025)