SZ
Shuangjia Zheng
cs.LGcs.AIbioinformaticsq-bio.BMProteinsDeep LearningComputational Biologyq-bio.QMbiophysicscs.CE
On Valency
published · living versionsW_62rs3ws9·v1 · currentpublished
ProteoCraft: Protein Design as Proposal-Verification Search
with Fang Wu, Hongbin Lin, Bingchen Duan, Yuchen Wang +22
1 version
Preprints & journals
93 papers in the corpus · 2018–2026Learning from Unverified Peers via Shared Residual Distillation2610.22080v1 · Feiyang Chen, Runze Ma, Zichen Wang et al.2026 · 0 citationsarXiv
ReTerm: Recovery Training for Self-Improving Terminal Agents2610.18484v2 · Wei Xie, Kaituo Feng, Shiming Fu et al.2026 · 0 citationsarXiv
La-Ribo: RNA Co-Design via Geometry-Latent Flow Matching2610.12236v1 · Runze Ma, Will Hua, Shuangjia Zheng2026 · 0 citationsarXiv
UniEvo-VL: An On-policy Self-Distillation Training Recipe for Multimodal Model Self-improvement2609.38721v1 · Fang Wu, Da Xing, Yanjie Huang et al.2026 · 0 citationsarXiv
Does Learning Protein Folding Generalize to Broader Reasoning?2609.38879v1 · Yong Liu, Zhanpeng Shi, Yizhou Dang et al.2026 · 0 citationsarXiv
M3OS: A Monte Carlo Graph Search-Orchestrated Multi-Agent LLM System for Evidence-Traced Molecular Optimization2609.34491v1 · Junjie Wang, Yaowei Jin, Ruohui Tang et al.2026 · 0 citationsarXiv
A systematic comparison of single-cell perturbation response prediction models.42715312 · Li, Lanxiang, You, Yue, Fu, Yunlin et al.2026 · 26 citationsScience advances. 2026;12(37):eaed3414
A blinded, prospective benchmark of in silico antibody discovery anchored to experimental affinity and developability.42618805 · Erasmus, M Frank, Bedinger, Daniel, Hopkins, Elizabeth et al.2026 · 0 citationsNature biotechnology. 2026
EnerBridge-DPO: Energy-Aware Markov Bridge Inverse Folding for Protein Sequence Design.42573394 · Rong, Dingyi, Lu, Haotian, Zhang, Xupeng et al.2026 · 0 citationsJournal of chemical information and modeling. 2026;66(15):9709-9720
Antigen-specific Antibody Multi-modal Foundation Model for Functional Antibody Design2607.20057v1 · Xiaoliang Shi, Zichen Wang, Runze Ma et al.2026 · 0 citationsarXiv
CACHE Challenge #4: Targeting the TKB Domain of the E3 ligase CBLB, an Immuno-Oncology Target10.26434/chemrxiv.15005792/v2 · Madhushika Silva, Oleksandra Herasymenko, Abd Al-Aziz A. Abu-Saleh et al.2026 · 0 citationsChemRxiv
OpenIO: An open framework for AI-native immunotherapy.42349428 · Wu, Yingcheng, Xiao, Hao, Jiang, Nan et al.2026 · 0 citationsCancer cell. 2026;44(7):1315-1320
ABRefine: An Accurate Antibody Structure Refinement Method by Equivariant Graph Transformer with Rigid Body Constraint.42152751 · Wang, Jinxian, Zhang, Ziqiao, Jing, Xiaoyang et al.2026 · 0 citationsJournal of medicinal chemistry. 2026;69(11):12925-12940
VeloTrace Reconciles Divergent Velocity and Trajectory in Single-cell Transcriptomics with Deep Neural ODE10.64898/2026.04.09.717458v1 · Cheng, H., Qiao, Y., Feng, Y. et al.2026 · 0 citationsbioRxiv
Accurate protein-protein interactions modeling through physics-informed geometric invariant learning.41896666 · Rao, Jiahua, Liu, Deqin, Zhou, Xiaolong et al.2026 · 1 citationCommunications biology. 2026;9(1)
Context-informed subgraph foundation models enable interpretable protein-function prediction.41861813 · Zhou, Zhuomin, Rao, Jiahua, Zhang, Zhongyue et al.2026 · 1 citationCell systems. 2026;17(4):101535
A Long-Context Generative Foundation Model Deciphers RNA Design Principles10.64898/2026.03.17.712398v2 · Huang, Y., Lv, G., Cheng, A. et al.2026 · 1 citationbioRxiv
InternAgent-1.5: A Unified Agentic Framework for Long-Horizon Autonomous Scientific Discovery2602.08990v1 · Shiyang Feng, Runmin Ma, Xiangchao Yan et al.2026 · 0 citationsarXiv
CACHE Challenge #3: Targeting the Nsp3 Macrodomain of SARS-CoV-2.41565251 · Herasymenko, Oleksandra, Silva, Madhushika, Correy, Galen J et al.2026 · 5 citationsJournal of chemical information and modeling. 2026;66(3):1566-1581
Efficient Protein Optimization via Structure-aware Hamiltonian Dynamics2601.11012v1 · Jiahao Wang, Shuangjia Zheng2026 · 0 citationsarXiv
Benchmarking all-atom biomolecular structure prediction with FoldBench.41345395 · Xu, Sheng, Feng, Qiantai, Qiao, Lifeng et al.2026 · 38 citationsNature communications. 2025;17(1):442
VCWorld: A Biological World Model for Virtual Cell Simulation2512.00306v2 · Zhijian Wei, Runze Ma, Zichen Wang et al.2025 · 2 citationsarXiv
NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction2511.02888v1 · Zhongmin Li, Runze Ma, Jiahao Tan et al.2025 · 1 citationarXiv
ODesign: A World Model for Biomolecular Interaction Design2510.22304v2 · Odin Zhang, Xujun Zhang, Haitao Lin et al.2025 · 3 citationsarXiv
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
From AI for Science to Agentic Science: A Survey on Autonomous Scientific Discovery2508.14111v2 · Jiaqi Wei, Yuejin Yang, Xiang Zhang et al.2025 · 6 citationsarXiv
Fitness aligned structural modeling enables scalable virtual screening with AuroBind2508.02137v1 · Zhongyue Zhang, Jiahua Rao, Jie Zhong et al.2025 · 0 citationsarXiv
A 3D pocket-aware lead optimization model with knowledge guidance and its application for discovery of new glutaminyl cyclase inhibitors.40669838 · Qiao, Anjie, Chen, Yuting, Xie, Junjie et al.2025 · 9 citationsBriefings in bioinformatics. 2025;26(4)
CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13.40539604 · Herasymenko, Oleksandra, Silva, Madhushika, Abu-Saleh, Abd Al-Aziz A et al.2025 · 20 citationsJournal of chemical information and modeling. 2025;65(13):6884-6898
EnerBridge-DPO: Energy-Guided Protein Inverse Folding with Markov Bridges and Direct Preference Optimization2506.09496v1 · Dingyi Rong, Haotian Lu, Wenzhuo Zheng et al.2025 · 1 citationarXiv
OriGene: A Self-Evolving Virtual Disease Biologist Automating Therapeutic Target Discovery10.1101/2025.06.03.657658v2 · Zhang, Z., Qiu, Z., Wu, Y. et al.2025 · 12 citationsbioRxiv
FoldBench: An All-atom Benchmark for Biomolecular Structure Prediction10.1101/2025.05.22.655600v1 · Xu, S., Feng, Q., Qiao, L. et al.2025 · 15 citationsbioRxiv
A 3D pocket-aware and affinity-guided diffusion model for lead optimization2504.21065v1 · Anjie Qiao, Junjie Xie, Weifeng Huang et al.2025 · 1 citationarXiv
Capturing Natural Evolution in Function-guided RNA Design via Genomic Foundation Models10.1101/2025.04.08.647793v1 · Zheng, S., Huang, Y., Zhang, B. et al.2025 · 1 citationbioRxiv
An Energy-Adaptive Elastic Equivariant Transformer Framework for Protein Structure Representation2503.16996v2 · Zhongyue Zhang, Runze Ma, Yanjie Huang et al.2025 · 0 citationsarXiv
RiboFlow: Conditional De Novo RNA Co-Design via Synergistic Flow Matching2503.17007v3 · Runze Ma, Zhongyue Zhang, Zichen Wang et al.2025 · 0 citationsarXiv
GerNA-Bind: Geometric-enhanced RNA-ligand Binding Specificity Prediction with Deep Learning10.1101/2025.02.15.638393v1 · Xia, Y., Li, J., Chu, Y.-T. et al.2025 · 2 citationsbioRxiv
NPC1L1 on pancreatic adenocarcinoma cell functions as a two-pronged checkpoint against antitumor activity.40098667 · Zi, Ruiyang, Shen, Kaicheng, Zheng, Pengfei et al.2025 · 7 citationsInnovation (Cambridge (Mass.)). 2025;6(3):100783
EnzymeCAGE: A Geometric Foundation Model for Enzyme Retrieval with Evolutionary Insights10.1101/2024.12.15.628585v1 · Liu, Y., Hua, C., Zeng, T. et al.2024 · 6 citationsbioRxiv
BindingGYM: A Large-Scale Mutational Dataset Toward Deciphering Protein-Protein Interactions10.1101/2024.12.03.626712v1 · Lu, W., Zhang, J., Gu, M. et al.2024 · 4 citationsbioRxiv
Reaction-conditioned De Novo Enzyme Design with GENzyme2411.16694v1 · Chenqing Hua, Jiarui Lu, Yong Liu et al.2024 · 6 citationsarXiv
CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein.39499532 · Li, Fengling, Ackloo, Suzanne, Arrowsmith, Cheryl H et al.2024 · 32 citationsJournal of chemical information and modeling. 2024;64(22):8521-8536
Deep generative design of RNA aptamers using structural predictions.39506080 · Wong, Felix, He, Dongchen, Krishnan, Aarti et al.2024 · 86 citationsNature computational science. 2024;4(11):829-839
Retrieval Augmented Diffusion Model for Structure-informed Antibody Design and Optimization2410.15040v2 · Zichen Wang, Yaokun Ji, Jianing Tian et al.2024 · 1 citationarXiv
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
RetroCaptioner: beyond attention in end-to-end retrosynthesis transformer via contrastively captioned learnable graph representation.39342389 · Liu, Xiaoyi, Ai, Chengwei, Yang, Hongpeng et al.2024 · 22 citationsBioinformatics (Oxford, England). 2024;40(9)
Developing BioNavi for Hybrid Retrosynthesis Planning.39055138 · Zeng, Tao, Jin, Zhehao, Zheng, Shuangjia et al.2024 · 24 citationsJACS Au. 2024;4(7):2492-2502
Cross-Modal Graph Contrastive Learning with Cellular Images.39031820 · Zheng, Shuangjia, Rao, Jiahua, Zhang, Jixian et al.2024 · 24 citationsAdvanced science (Weinheim, Baden-Wurttemberg, Germany). 2024;11(32):e2404845
AlphaFold3, a secret sauce for predicting mutational effects on protein-protein interactions10.1101/2024.05.25.595871v1 · Lu, W., Zhang, J., Rao, J. et al.2024 · 22 citationsbioRxiv
A variational expectation-maximization framework for balanced multi-scale learning of protein and drug interactions.38796523 · Rao, Jiahua, Xie, Jiancong, Yuan, Qianmu et al.2024 · 25 citationsNature communications. 2024;15(1):4476
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