Improving AlphaFold3 by Engineering MSA and Template Inputs (opens in new tab)

AlphaFold3 introduces a unified framework for predicting the structures and interaction of several biomolecules including single-chain protein monomers, multi-chain protein multimers, and protein-ligand complexes. While it achieves the state-of-the-art performance in most predictions, its prediction accuracy depends on the quality of multiple sequence alignment (MSA) and structural template inputs. There are few works of using customized MSAs and templates to improve AlphaFold3. In this work,...