AlphaFold-Multimer
A-Google DeepMind
Complex PredictionProtein-Protein Interactionrestricted
Updated 1 month agoNextIn take
AlphaFold-Multimer is the reliable workhorse that most structural biology labs still use daily — it's not the frontier anymore, but the tooling ecosystem around it is unmatched.
Specifications
| Architecture | AlphaFold2 with multi-chain modifications for complex prediction |
| Parameters | ~400M |
| Training Data | PDB multimer structures, UniRef, BFD |
| License | Code open-source (Apache 2.0) but model use restricted by DeepMind terms. Superseded by AF3 for new work. |
| Hardware | 1x A100 40GB+ for most complexes, more for large assemblies |
| Inference Cost | Self-hosted — moderate GPU cost, slower than single-chain AF2 |
| API Available | Yes |
| Weights Available | No |
Benchmark Performance
When to Use This
- +Protein-protein interaction prediction with established tooling
- +When you need community support and well-tested pipelines
When NOT to Use This
- −New projects where AF3 or Boltz-1 would give better results
- −Ligand docking — not designed for small molecules
Production Readiness
production
Known Users
- Thousands of academic and industry labs worldwide
- Isomorphic Labs
Grade Rationale
A-
Was the best complex prediction tool before AF3 arrived. Still reliable and battle-tested, with a larger user base and more community tooling than AF3. A- because it's proven but no longer state-of-the-art.
Sources
Update History
2026-02-10Initial entry