4 accepted papers
Molecular docking is a key task in computational biology that has attracted increasing interest from the machine learning community. While existing methods have achieved success, they generally treat each protein-ligand pair in isolation. Inspired by the biochemical observation that ligands binding…
Despite the striking success of general protein folding models such as AlphaFold2 (AF2), the accurate computational modeling of antibody-antigen complexes remains a challenging task. In this paper, we first analyze AF2's primary loss function, known as the Frame Aligned Point Error (FAPE), and raise…
Point cloud data is ubiquitous in scientific fields. Recently, geometric deep learning (GDL) has been widely applied to solve prediction tasks with such data. However, GDL models are often complicated and hardly interpretable, which poses concerns to scientists who are to deploy these models in scie…
Targeted protein degradation techniques, such as PROteolysis TArgeting Chimeras (PROTACs), have emerged as powerful tools for selectively removing disease-causing proteins. One challenging problem in this field is designing a linker to connect different molecular fragments to form a stable drug-cand…