AlphaFast: High-throughput AlphaFold 3 via GPU-accelerated MSA construction
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.
Fields of Study & Subjects
Genomics and Phylogenetic Studies
Protein Structure and Dynamics
Genomics and Chromatin Dynamics
Publication details
- Journal / source
- bioRxiv (Cold Spring Harbor Laboratory)
- Publisher
- openRxiv
- Publication date
- 18 February 2026
- Language
- EN
- Document type
- Preprint