AlphaFold 3 vs RoseTTAFold vs ESMFold vs OmegaFold
Protein Structure Prediction Comparison
Comparison of 4 AI protein structure prediction tools — accuracy, speed, complex modeling, availability, and use case.
AlphaFold 3RoseTTAFoldESMFoldOmegaFold
Full Specification Comparison
| Specification | AlphaFold 3 | RoseTTAFold | ESMFold | OmegaFold |
|---|---|---|---|---|
| Protein-Ligand | Yes | No | No | No |
| Accuracy (GDT) | Highest | High | Moderate | Good |
| Speed | ~1 min/structure | ~10 min | ~9 sec | ~30 sec |
| Open Source | Limited (server) | Yes | Yes | Yes |
| Protein-Protein | Yes | Yes | No | No |
| GPU Required | Yes | Yes | Yes | Yes |
| Best For | Drug discovery | Complexes | Fast prediction | No-MSA prediction |
Expert Verdict
AlphaFold 3 models protein-ligand interactions and is the most accurate; ESMFold is 60x faster for single-chain; RoseTTAFold offers the best open-source alternative; OmegaFold excels with sparse MSA.
Subject Breakdown
AlphaFold 3
3 Category Wins
- ★ Protein-Ligand: Yes
- ★ Accuracy (GDT): Highest
- ★ Protein-Protein: Yes
RoseTTAFold
1 Category Wins
- ★ Open Source: Yes
ESMFold
1 Category Wins
- ★ Speed: ~9 sec
OmegaFold
0 Category Wins