AlphaFast: GPU-Accelerated MSA Construction for AlphaFold 3

AlphaFast is a framework designed to accelerate the Multiple Sequence Alignment (MSA) construction step for AlphaFold 3 (AF3) by integrating GPU-accelerated MMseqs2 search. It significantly reduces end-to-end runtime while maintaining structural accuracy, providing high-throughput biomolecular prediction.