33 citations · 83 across the 17 of their papers we have counts for
9 papers · 1 filter
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…