OZ
Odin Zhang
q-bio.BMcs.LGcs.AIDrug DiscoveryProteinsDeep LearningDrug DesignbiochemistrybioinformaticsNeural Networks, Computer
On Valency
published · living versionsW_ga2kwdz9·v1 · currentpublished
RiboBridge: protein-conditioned de novo RNA binder structure design
with Zhou Zhang, Hanqun Cao, Minghao Sun, Yang Zhang +3
1 version
Preprints & journals
51 papers in the corpus · 2022–2026RiboBridge: protein-conditioned de novo RNA binder structure design2610.30668v1 · Zhou Zhang, Hanqun Cao, Minghao Sun et al.2026 · 0 citationsarXivon Valency
Atomic functional site scaffolding in biopolymers with RFdiffusion3.42879533 · Butcher, Jasper, Krishna, Rohith, Mitra, Raktim et al.2026 · 2 citationsScience (New York, N.Y.). 2026:eaeh2982
NACraft: Programmatic nucleic-acid aptamer design via all-atom structure-model feedback10.64898/2026.08.15.744087v1 · Zhu, H., Wang, J., Zhao, W. et al.2026 · 0 citationsbioRxiv
EpiBench: Can LLMs Understand Epitopes for Antibody Drug Discovery?2608.06022v1 · Zirui Wang, Jiaqi Wang, Qinghan Wang et al.2026 · 0 citationsarXiv
ProphDR: An Interpretable Deep Learning Model for Predicting Cancer Drug Response via Multi-Omics and Cross-Attention Mechanisms.42441428 · Zeng, Yundian, Ye, Qing, Wang, Jike et al.2026 · 0 citationsJournal of chemical information and modeling. 2026;66(14):7874-7888
Facilitating structure-based drug discovery with an artificial intelligence-driven virtual screening platform.42342989 · Gu, Shukai, Zhang, Xujun, Xiao, Mengwu et al.2026 · 1 citationNature protocols. 2026;21(11):5548-5567
Revisiting Target-Aware de novo Molecular Generation with TarPass: Between Rational Design and Texas Sharpshooter.42018135 · Qin, Rui, Chen, Zijie, Li, Yurong et al.2026 · 0 citationsAdvanced science (Weinheim, Baden-Wurttemberg, Germany). 2026;13(40):e75411
Accurate and task-agnostic modeling of enzymatic reactions through multimodal relational learning.42453428 · Huang, Yuansheng, Li, Lanqing, Qian, Wenjia et al.2026 · 0 citationsActa pharmaceutica Sinica. B. 2026;16(7):4051-4066
MetalloDock: Decoding Metalloprotein-Ligand Interactions via Physics-Aware Deep Learning for Metalloprotein Drug Discovery.41527511 · Zhang, Hui, Zhang, Xujun, Su, Qun et al.2026 · 7 citationsJournal of the American Chemical Society. 2026;148(3):3086-3101
Unlocking the application potential of AlphaFold3-like approaches in virtual screening.41403459 · Shen, Chao, Zhang, Xujun, Gu, Shukai et al.2025 · 16 citationsChemical science. 2025
A virtual platform for automated hybrid organic-enzymatic synthesis planning.41298428 · Wang, Xiaorui, Yin, Xiaodan, Zhang, Xujun et al.2025 · 3 citationsNature communications. 2025;16(1):10929
De novo Design of All-atom Biomolecular Interactions with RFdiffusion3.41000976 · Butcher, Jasper, Krishna, Rohith, Mitra, Raktim et al.2025 · 73 citationsbioRxiv : the preprint server for biology. 2025
ECloudGen: leveraging electron clouds as a latent variable to scale up structure-based molecular design.41094041 · Zhang, Odin, Jin, Jieyu, Wu, Zhenxing et al.2025 · 7 citationsNature computational science. 2025;5(11):1017-1028
Harnessing deep statistical potential for biophysical scoring of protein-peptide interactions.41034399 · Jiang, De-Jun, Zhao, Hui-Feng, Du, Hong-Yan et al.2026 · 0 citationsActa pharmacologica Sinica. 2026;47(2):518-532
Graph Neural Networks in Modern AI-Aided Drug Discovery.40959983 · Zhang, Odin, Lin, Haitao, Zhang, Xujun et al.2025 · 91 citationsChemical reviews. 2025;125(20):10001-10103
Accelerating Biomolecular Modeling with AtomWorks and RF3.40832246 · Corley, Nathaniel, Mathis, Simon, Krishna, Rohith et al.2025 · 43 citationsbioRxiv : the preprint server for biology. 2025
Fitness aligned structural modeling enables scalable virtual screening with AuroBind2508.02137v1 · Zhongyue Zhang, Jiahua Rao, Jie Zhong et al.2025 · 0 citationsarXiv
HawkDock version 2: an updated web server to predict and analyze the structures of protein-protein complexes.40326522 · Zhang, Xujun, Jiang, Linlong, Weng, Gaoqi et al.2025 · 46 citationsNucleic acids research. 2025;53(W1):W306-W315
Token-Mol 1.0: tokenized drug design with large language models.40360500 · Wang, Jike, Qin, Rui, Wang, Mingyang et al.2025 · 26 citationsNature communications. 2025;16(1):4416
AutoLoop: a novel autoregressive deep learning method for protein loop prediction with high accuracy2505.03121v1 · Tianyue Wang, Xujun Zhang, Langcheng Wang et al.2025 · 0 citationsarXiv
Structure-based design of anticancer drugs based on β-elemene: Research foundations and development potential.41399412 · Chen, Haiyi, Yu, Yuntao, Hu, Chenghong et al.2025 · 3 citationsJournal of pharmaceutical analysis. 2025;15(11):101325
Correction: DiffBP: generative diffusion of 3D molecules for target protein binding.40144506 · Lin, Haitao, Huang, Yufei, Zhang, Odin et al.2025 · 3 citationsChemical science. 2025;16(15):6523
Correction: FragGen: towards 3D geometry reliable fragment-based molecular generation.39713761 · Zhang, Odin, Huang, Yufei, Chen, Shicheng et al.2025 · 0 citationsChemical science. 2025;16(3):1467
Durian: A Comprehensive Benchmark for Structure-Based 3D Molecular Generation.39681323 · Nie, Dou, Zhao, Huifeng, Zhang, Odin et al.2025 · 16 citationsJournal of chemical information and modeling. 2025;65(1):173-186
Descriptor-Free Collective Variables from Geometric Graph Neural Networks.39665183 · Zhang, Jintu, Bonati, Luigi, Trizio, Enrico et al.2024 · 33 citationsJournal of chemical theory and computation. 2024;20(24):10787-10797
3DSMILES-GPT: 3D molecular pocket-based generation with token-only large language model.39664804 · Wang, Jike, Luo, Hao, Qin, Rui et al.2025 · 42 citationsChemical science. 2025;16(2):637-648
DiffBP: generative diffusion of 3D molecules for target protein binding.39713760 · Lin, Haitao, Huang, Yufei, Zhang, Odin et al.2025 · 78 citationsChemical science. 2025;16(3):1417-1431
ClickGen: Directed exploration of synthesizable chemical space via modular reactions and reinforcement learning.39578485 · Wang, Mingyang, Li, Shuai, Wang, Jike et al.2024 · 34 citationsNature communications. 2024;15(1):10127
Reaction-conditioned De Novo Enzyme Design with GENzyme2411.16694v1 · Chenqing Hua, Jiarui Lu, Yong Liu et al.2024 · 6 citationsarXiv
Deep Lead Optimization: Leveraging Generative AI for Structural Modification.39499822 · Zhang, Odin, Lin, Haitao, Zhang, Hui et al.2024 · 56 citationsJournal of the American Chemical Society. 2024;146(46):31357-31370
CovalentInDB 2.0: an updated comprehensive database for structure-based and ligand-based covalent inhibitor design and screening.39441070 · Du, Hongyan, Zhang, Xujun, Wu, Zhenxing et al.2025 · 32 citationsNucleic acids research. 2025;53(D1):D1322-D1327
FragGen: towards 3D geometry reliable fragment-based molecular generation.39568888 · Zhang, Odin, Huang, Yufei, Cheng, Shichen et al.2024 · 16 citationsChemical science. 2024;15(46):19452-19465
EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamics2410.00327v1 · Chenqing Hua, Yong Liu, Dinghuai Zhang et al.2024 · 6 citationsarXiv
Enabling target-aware molecule generation to follow multi objectives with Pareto MCTS.39223327 · Yang, Yaodong, Chen, Guangyong, Li, Jinpeng et al.2024 · 11 citationsCommunications biology. 2024;7(1):1074
Multi-modal deep learning enables efficient and accurate annotation of enzymatic active sites.39187482 · Wang, Xiaorui, Yin, Xiaodan, Jiang, Dejun et al.2024 · 43 citationsNature communications. 2024;15(1):7348
Highly Accurate and Efficient Deep Learning Paradigm for Full-Atom Protein Loop Modeling with KarmaLoop.39055686 · Wang, Tianyue, Zhang, Xujun, Zhang, Odin et al.2024 · 4 citationsResearch (Washington, D.C.). 2024;7:0408
Token-Mol 1.0: Tokenized drug design with large language model2407.07930v2 · Jike Wang, Rui Qin, Mingyang Wang et al.2024 · 2 citationsarXiv
3D Molecular Pocket-based Generation with Token-only Large Language Model10.26434/chemrxiv-2024-0ckgt-v2 · Jike Wang, Hao Luo, Rui Qin et al.2024 · 1 citationChemRxiv
DrugFlow: An AI-Driven One-Stop Platform for Innovative Drug Discovery.38920405 · Shen, Chao, Song, Jianfei, Hsieh, Chang-Yu et al.2024 · 51 citationsJournal of chemical information and modeling. 2024;64(14):5381-5391
CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph2406.10840v3 · Haitao Lin, Guojiang Zhao, Odin Zhang et al.2024 · 4 citationsarXiv
Combining Transition Path Sampling with Data-Driven Collective Variables through a Reactivity-Biased Shooting Algorithm.38801759 · Zhang, Jintu, Zhang, Odin, Bonati, Luigi et al.2024 · 14 citationsJournal of chemical theory and computation. 2024;20(11):4523-4532
GeoAB: Towards Realistic Antibody Design and Reliable Affinity Maturation10.1101/2024.05.15.594274v2 · LIN, H., Wu, L., Yufei, H. et al.2024 · 2 citationsbioRxiv
Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation2404.00014v1 · Odin Zhang, Yufei Huang, Shichen Cheng et al.2024 · 3 citationsarXiv
PPFlow: Target-aware Peptide Design with Torsional Flow Matching2405.06642v4 · Haitao Lin, Odin Zhang, Huifeng Zhao et al.2024 · 8 citationsarXiv
Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge2402.11459v2 · Yufei Huang, Odin Zhang, Lirong Wu et al.2024 · 6 citationsarXiv
Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency.38171930 · Wang, Tianyue, Wang, Langcheng, Zhang, Xujun et al.2024 · 17 citationsBriefings in bioinformatics. 2023;25(1)
A flexible data-free framework for structure-based de novo drug design with reinforcement learning.37969589 · Du, Hongyan, Jiang, Dejun, Zhang, Odin et al.2026 · 23 citationsChemical science. 2023;14(43):12166-12181
Protein 3D Graph Structure Learning for Robust Structure-based Protein Property Prediction2310.11466v2 · Yufei Huang, Siyuan Li, Jin Su et al.2023 · 6 citationsarXiv
Learning on topological surface and geometric structure for 3D molecular generation.38177756 · Zhang, Odin, Wang, Tianyue, Weng, Gaoqi et al.2024 · 58 citationsNature computational science. 2023;3(10):849-859
Efficient and accurate large library ligand docking with KarmaDock.38177786 · Zhang, Xujun, Zhang, Odin, Shen, Chao et al.2024 · 170 citationsNature computational science. 2023;3(9):789-804
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