AlphaFast: High-throughput AlphaFold 3 via GPU-accelerated MSA construction

Benjamin C. Perry, Jeonghyeon Kim, Philip Romero

Keywords: alphafold3, fast, acceleration, alphafast, protein folding, optimization, systems engineering, structural biology, biological ai, proteomics, high throughput screening, iteractomics, protein engineering

Abstract:

AlphaFold 3 (AF3) enables accurate biomolecular modeling but is limited by slow, CPU-bound multiple sequence alignment (MSA) generation. We introduce AlphaFast, a drop-in framework that integrates GPU-accelerated MMseqs2 sequence search to remove this bottleneck. AlphaFast achieves a 68.5× speedup in MSA construction and a 22.8× reduction in end-to-end runtime on a single GPU, and delivers predictions in 8 seconds per input on four GPUs while maintaining indistinguishable structural accuracy. A serverless deployment enables structure prediction for as little as \$0.035 per input.
Code is available at https://github.com/RomeroLab/alphafast

Submission Number: 70