3 papers
cs.LG2026
Learning Mechanistic Reasoning for Chemical Reactions with Large Language Models
Xingyu Dang, Haocheng Tang, Junmei Wang +1
Reaction mechanisms consist of the step-by-step sequences of elementary reactions that explain chemical transformations. Learning the mechanism logic is therefore essential for enh…
q-bio.BM2025
Apo2Mol: 3D Molecule Generation via Dynamic Pocket-Aware Diffusion Models
Xinzhe Zheng, Shiyu Jiang, Gustavo Seabra +2
Deep generative models are rapidly advancing structure-based drug design, offering substantial promise for generating small molecule ligands that bind to specific protein targets.…
cs.LG2025
DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction
Yupu Zhang, Zelin Xu, Tingsong Xiao +4
Predicting the binding affinity of protein-ligand complexes plays a vital role in drug discovery. Unfortunately, progress has been hindered by the lack of large-scale and high-qual…