776 citations · 1.4k across the 18 of their papers we have counts for
18 papers
Atomic Trajectory Modeling with State Space Models for Biomolecular Dynamics
Liang Shi, Jiarui Lu, Junqi Liu +3
Understanding the dynamic behavior of biomolecules is fundamental to elucidating biological function and facilitating drug discovery. While Molecular Dynamics (MD) simulations prov…
Property-driven Protein Inverse Folding With Multi-Objective Preference Alignment
Xiaoyang Hou, Junqi Liu, Chence Shi +3
Protein sequence design must balance designability, defined as the ability to recover a target backbone, with multiple, often competing, developability properties such as solubilit…
Structure Language Models for Protein Conformation Generation
Jiarui Lu, Xiaoyin Chen, Stephen Zhewen Lu +4
Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is crucial for advancing drug discovery. Tradi…
Design of Ligand-Binding Proteins with Atomic Flow Matching
Junqi Liu, Shaoning Li, Chence Shi +2
Designing novel proteins that bind to small molecules is a long-standing challenge in computational biology, with applications in developing catalysts, biosensors, and more. Curren…
Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations
Jiarui Lu, Zuobai Zhang, Bozitao Zhong +2
The protein dynamics are common and important for their biological functions and properties, the study of which usually involves time-consuming molecular dynamics (MD) simulations…
Protein Sequence and Structure Co-Design with Equivariant Translation
Chence Shi, Chuanrui Wang, Jiarui Lu +2
Proteins are macromolecules that perform essential functions in all living organisms. Designing novel proteins with specific structures and desired functions has been a long-standi…