4 papers
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…
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…