Shuangjia Zheng

NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction

VCWorld: A Biological World Model for Virtual Cell Simulation

Self-Tooling Agent: Dynamically Extending Agent Capabilities through Scientific Tool Synthesis and Invocation

EnerBridge-DPO: Energy-Guided Protein Inverse Folding with Markov Bridges and Direct Preference Optimization

Repurposing AlphaFold3-like Protein Folding Models for Antibody Sequence and Structure Co-design

RiboFlow: Conditional De Novo RNA Co-Design via Synergistic Flow Matching

Accurately Predicting Protein Mutational Effects via a Hierarchical Many-Body Attention Network

Retrieval Augmented Diffusion Model for Structure-informed Antibody Design and Optimization

$E^3$former: An Adaptive Energy-Aware Elastic Equivariant Transformer Model For Protein Representation Learning

EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamics

Efficient Protein Optimization via Structure-aware Hamiltonian Dynamics