33 citations · 83 across the 17 of their papers we have counts for
19 papers
RiboBridge: protein-conditioned de novo RNA binder structure design
Zhou Zhang, Hanqun Cao, Minghao Sun +5
Designing RNA molecules that bind to target protein structures requires generating both an RNA conformation and its bound complex geometry, without assuming a predefined binding si…
CODesign: Consistency from Data to Trajectory in All-Atom Protein Binder Co-Design
Yuanle Mo, Bo Qiang, Haitao Lin +4
The central challenge in de novo protein design is generating plausible, mutually compatible structures and sequences, such that each designed sequence folds into its intended stru…
ADMET-EvO: a self-evolving scientific agent for sustained research across heterogeneous tasks
Yiling Zhou, Yilin Wang, Jianmin Wang +8
Scientific agents can move beyond automated model building by using accumulated evidence to revise both their questions and experimental strategies. The challenge is sustaining thi…
EpiBench: Can LLMs Understand Epitopes for Antibody Drug Discovery?
Zirui Wang, Jiaqi Wang, Qinghan Wang +4
Epitopes determine where antibodies bind antigens and shape downstream therapeutic properties such as functional blockade and escape resistance, making epitope understanding centra…
NanoResearch: Co-Evolving Skills, Memory, and Policy for Personalized Research Automation
Jinhang Xu, Qiyuan Zhu, Yujun Wu +11
LLM-powered multi-agent systems can now automate the full research pipeline from ideation to paper writing, but a fundamental question remains: automation for whom? Researchers ope…
Graph Neural Networks in Modern AI-aided Drug Discovery
Odin Zhang, Haitao Lin, Xujun Zhang +9
Graph neural networks (GNNs), as topology/structure-aware models within deep learning, have emerged as powerful tools for AI-aided drug discovery (AIDD). By directly operating on m…
AutoLoop: a novel autoregressive deep learning method for protein loop prediction with high accuracy
Tianyue Wang, Xujun Zhang, Langcheng Wang +12
Protein structure prediction is a critical and longstanding challenge in biology, garnering widespread interest due to its significance in understanding biological processes. A par…
Descriptors-free Collective Variables From Geometric Graph Neural Networks
Jintu Zhang, Luigi Bonati, Enrico Trizio +4
Enhanced sampling simulations make the computational study of rare events feasible. A large family of such methods crucially depends on the definition of some collective variables…
Token-Mol 1.0: Tokenized drug design with large language model
Jike Wang, Rui Qin, Mingyang Wang +17
Significant interests have recently risen in leveraging sequence-based large language models (LLMs) for drug design. However, most current applications of LLMs in drug discovery la…
Rethinking the Diffusion Models for Numerical Tabular Data Imputation from the Perspective of Wasserstein Gradient Flow
Zhichao Chen, Haoxuan Li, Fangyikang Wang +5
Diffusion models (DMs) have gained attention in Missing Data Imputation (MDI), but there remain two long-neglected issues to be addressed: (1). Inaccurate Imputation, which arises…
CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph
Haitao Lin, Guojiang Zhao, Odin Zhang +7
Structure-based drug design (SBDD) aims to generate potential drugs that can bind to a target protein and is greatly expedited by the aid of AI techniques in generative models. How…
PPFlow: Target-aware Peptide Design with Torsional Flow Matching
Haitao Lin, Odin Zhang, Huifeng Zhao +5
Therapeutic peptides have proven to have great pharmaceutical value and potential in recent decades. However, methods of AI-assisted peptide drug discovery are not fully explored.…
Deep Lead Optimization: Leveraging Generative AI for Structural Modification
Odin Zhang, Haitao Lin, Hui Zhang +7
The idea of using deep-learning-based molecular generation to accelerate discovery of drug candidates has attracted extraordinary attention, and many deep generative models have be…
Combining transition path sampling with data-driven collective variables through a reactivity-biased shooting algorithm
Jintu Zhang, Odin Zhang, Luigi Bonati +1
Rare event sampling is a central problem in modern computational chemistry research. Among the existing methods, transition path sampling (TPS) can generate unbiased representation…
Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation
Odin Zhang, Yufei Huang, Shichen Cheng +14
Most earlier 3D structure-based molecular generation approaches follow an atom-wise paradigm, incrementally adding atoms to a partially built molecular fragment within protein pock…
Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge
Yufei Huang, Odin Zhang, Lirong Wu +5
Accurate prediction of protein-ligand binding structures, a task known as molecular docking is crucial for drug design but remains challenging. While deep learning has shown promis…
Protein 3D Graph Structure Learning for Robust Structure-based Protein Property Prediction
Yufei Huang, Siyuan Li, Jin Su +9
Protein structure-based property prediction has emerged as a promising approach for various biological tasks, such as protein function prediction and sub-cellular location estimati…
Highly accurate and efficient deep learning paradigm for full-atom protein loop modeling with KarmaLoop
Tianyue Wang, Xujun Zhang, Odin Zhang +5
Protein loop modeling is the most challenging yet highly non-trivial task in protein structure prediction. Despite recent progress, existing methods including knowledge-based, ab i…
DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding
Haitao Lin, Yufei Huang, Odin Zhang +7
Generating molecules that bind to specific proteins is an important but challenging task in drug discovery. Previous works usually generate atoms in an auto-regressive way, where e…