Yafeng Deng

Pharmaceutical Biotechnology (Czechia) — Czech Republic

Computer Science · Physical Sciences

25h-index2.6kcitations68works15.82yr avg
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Research Topics

Computational Drug Discovery Methods(40), Machine Learning in Materials Science(19), Protein Structure and Dynamics(14), Face and Expression Recognition(8), Metabolomics and Mass Spectrometry Studies(8)

Publications68 total

NMRMind: A Transformer-Based Model Enabling the Elucidation from Multidimensional NMR to Structures
Analytical Chemistry·2025· 1 cited
RSGPT: a generative transformer model for retrosynthesis planning pre-trained on ten billion datapoints
Nature Communications·2025· 2 citedOpen Access
HiCLR: Knowledge-Induced Hierarchical Contrastive Learning with Retrosynthesis Prediction Yields a Reaction Foundation Model
JACS Au·2025Open Access
A Knowledge‐Guided Graph Learning Approach Bridging Phenotype‐ and Target‐Based Drug Discovery
Advanced Science·2025· 6 citedOpen Access
Discovery of antimicrobial peptides with notable antibacterial potency by an LLM-based foundation model
Science Advances·2025· 58 citedOpen Access
Syn-MolOpt: a synthesis planning-driven molecular optimization method using data-derived functional reaction templates
Journal of Cheminformatics·2025· 3 citedOpen Access
Bidirectional Chemical Intelligent Net: A unified deep learning–based framework for predicting chemical reaction
Chinese Chemical Letters·2025· 2 cited
Benchmarking AI-powered docking methods from the perspective of virtual screening
Nature Machine Intelligence·2025· 24 cited
Improving the Reliability of Language Model-Predicted Structures as Docking Targets through Geometric Graph Learning
Journal of Medicinal Chemistry·2025· 7 cited
TRAP: a contrastive learning-enhanced framework for robust TCR–pMHC binding prediction with improved generalizability
Chemical Science·2025· 3 citedOpen Access
Molecular mechanism of pancreatic ductal adenocarcinoma: The heterogeneity of cancer-associated fibroblasts and key signaling pathways
World Journal of Clinical Oncology·2024· 3 citedOpen Access
ClickGen: Directed exploration of synthesizable chemical space via modular reactions and reinforcement learning
Nature Communications·2024· 20 citedOpen Access
Leveraging language model for advanced multiproperty molecular optimization via prompt engineering
Nature Machine Intelligence·2024· 30 cited
PROTAC-DB 3.0: an updated database of PROTACs with extended pharmacokinetic parameters
Nucleic Acids Research·2024· 73 citedOpen Access
Multi-modal deep learning enables efficient and accurate annotation of enzymatic active sites
Nature Communications·2024· 34 citedOpen Access
Bidirectional Chemical Intelligent Net: A unified deep learning–based framework for predicting chemical reactions
2024Open Access
Discovery of novel antimicrobial peptides with notable antibacterial potency by a LLM-based foundation model
arXiv (Cornell University)·2024Open Access
DrugFlow: An AI-Driven One-Stop Platform for Innovative Drug Discovery
Journal of Chemical Information and Modeling·2024· 33 cited
Deep-learning-based prediction framework for protein-peptide interactions with structure generation pipeline
Cell Reports Physical Science·2024· 16 citedOpen Access
AAVDiff: Experimental Validation of Enhanced Viability and Diversity in Recombinant Adeno-Associated Virus (AAV) Capsids through Diffusion Generation
arXiv (Cornell University)·2024Open Access
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Frequent Co-authors

Tingjun Hou(34), Chang‐Yu Hsieh(26), Yu Kang(19), Peichen Pan(14), Jike Wang(13), Hongyan Du(12), Dejun Jiang(11), Dongsheng Cao(10), Chao Shen(9), Xujun Zhang(9), Zhenhua Wu(8), Odin Zhang(8), Xiaorui Wang(8), Dan Li(7), Xiangyang Ji(7), Huifeng Zhao(6), Gaoqi Weng(5), Heng Cai(5), Xiaojian Wang(5), Zhenxing Wu(5)