AlphaDesign: A graph protein design method and benchmark on AlphaFoldDB

Understand

While DeepMind has tentatively solved protein folding, its inverse problem -- protein design which predicts protein sequences from their 3D structures -- still faces significant challenges.

• Particularly, the lack of large-scale standardized benchmark and poor accuray hinder the research progress.
• In order to standardize comparisons and draw more research interest, we use AlphaFold DB, one of the world's largest protein structure databases, to establish a new graph-based benchmark -- AlphaDesign.
• Based on AlphaDesign, we propose a new method called ADesign to improve accuracy by introducing protein angles as new features, using a simplified graph transformer encoder (SGT), and proposing a confidence-aware protein decoder (CPD).