3 papers
cs.AI2026
Probe Before You Edit: Probing-Guided Molecular Optimization for LLM Agents in Structure-Based Drug Design
Zaifei Yang, Weiyu Chen, Yaqing Wang +1
Structure-based drug design increasingly employs LLM agents to iteratively refine ligands against a target pocket, yet a viable ligand must satisfy two often-conflicting objectives…
q-bio.QM2026
Enhancing Protein-Protein Interaction Prediction with Hierarchical Motif-based Multimodal Protein Embedding
Zaifei Yang, Samuel Ping-Man Choi, James Kwok
Protein-protein interactions (PPIs) are essential for many biological processes. However, existing PPI prediction approaches suffer from two major limitations: they overlook the hi…
q-bio.BM2025
KnowMol: Advancing Molecular Large Language Models with Multi-Level Chemical Knowledge
Zaifei Yang, Hong Chang, Ruibing Hou +2
The molecular large language models have garnered widespread attention due to their promising potential on molecular applications. However, current molecular large language models…