3 papers
q-bio.QM2025
Protein Structure Tokenization: Benchmarking and New Recipe
Xinyu Yuan, Zichen Wang, Marcus Collins +1
Recent years have witnessed a surge in the development of protein structural tokenization methods, which chunk protein 3D structures into discrete or continuous representations. St…
cs.LG2025
AffinityFlow: Guided Flows for Antibody Affinity Maturation
Can Chen, Karla-Luise Herpoldt, Chenchao Zhao +4
Antibodies are widely used as therapeutics, but their development requires costly affinity maturation, involving iterative mutations to enhance binding affinity.This paper explores…
cs.LG2024
Pushing the Limits of All-Atom Geometric Graph Neural Networks: Pre-Training, Scaling and Zero-Shot Transfer
Zihan Pengmei, Zhengyuan Shen, Zichen Wang +2
Constructing transferable descriptors for conformation representation of molecular and biological systems finds numerous applications in drug discovery, learning-based molecular dy…