Transformers
Safetensors
English
esmfold2
biology
esm
protein
protein-structure-prediction
structure-prediction
protein-design
3d-structure
confidence-estimation
molecular-dynamics
Instructions to use biohub/ESMFold2-Fast with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Transformers
How to use biohub/ESMFold2-Fast with Transformers:
# Load model directly from transformers import AutoTokenizer, AutoModel tokenizer = AutoTokenizer.from_pretrained("biohub/ESMFold2-Fast") model = AutoModel.from_pretrained("biohub/ESMFold2-Fast", device_map="auto") - Notebooks
- Google Colab
- Kaggle
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license: mit
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# Model Card for
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## Model Details
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The model predicts high-resolution, all-atom 3D protein structures directly from amino acid sequences, with optional multiple sequence alignment (MSA) input for enhanced accuracy on challenging targets. The model outputs comprehensive structural information including all-atom coordinates (backbone and side chains), confidence metrics (pLDDT, pAE, pTM, iPTM), and optional distogram predictions for detailed analysis of predicted structures. Unlike ESMFold,
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For additional information, visit the [Biohub Platform](https://biohub.ai) for no-code tools, step-by-step tutorial notebooks, and detailed information on the models.
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- This efficient sampling strategy significantly reduces computational cost while maintaining accuracy
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**4\. Optional MSA Encoder (
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- Processes multiple sequence alignments to extract evolutionary information
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| Model | MSA Conditioning | Description | Data Cutoff |
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**Confidence Head (optional, for inference):**
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### Primary Use Cases
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#### **Complex biomolecular interactions**
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## Performance Metrics
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Refer to the [paper](https://biohub.ai/papers/esmc.pdf) for details on additional performance metrics.
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Many people on the Biohub AI Research team and prior EvolutionaryScale team contributed to the development of this model. It would not have been possible without them.
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license: mit
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# Model Card for ESMFold2-Fast
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## Model Details
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ESMFold2 is a state-of-the-art protein structure prediction model that combines ESMC (6B parameter) language model representations with a diffusion-based structure prediction architecture inspired by AlphaFold3.
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The model predicts high-resolution, all-atom 3D protein structures directly from amino acid sequences, with optional multiple sequence alignment (MSA) input for enhanced accuracy on challenging targets. The model outputs comprehensive structural information including all-atom coordinates (backbone and side chains), confidence metrics (pLDDT, pAE, pTM, iPTM), and optional distogram predictions for detailed analysis of predicted structures. Unlike ESMFold, ESMFold2 is able to predict structures for all biomolecules, including small molecules, DNA, RNA, and modified amino acids.
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ESMFold2-Fast is an Inference optimized single-sequence structure prediction model and is not MSA conditioned.
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For additional information, visit the [Biohub Platform](https://biohub.ai) for no-code tools, step-by-step tutorial notebooks, and detailed information on the models.
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- This efficient sampling strategy significantly reduces computational cost while maintaining accuracy
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**4\. Optional MSA Encoder (ESMFold2 MSA variant):**
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- Processes multiple sequence alignments to extract evolutionary information
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| Model | MSA Conditioning | Description | Data Cutoff |
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| [ESMFold2-fast](https://huggingface.co/biohub/esmfold2-fast) | No | Inference optimized single-sequence structure prediction model | June 2025, older cutoff is Sept 2021 |
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| [ESMFold2](https://huggingface.co/biohub/esmfold2) | Yes | Large model, capable of either single-sequence or MSA conditioned structure prediction for improved accuracy on difficult targets | June 2025, older cutoff is Sept 2021 |
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**Confidence Head (optional, for inference):**
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### Primary Use Cases
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ESMFold2-Fast is designed to handle a wide range of structural prediction tasks, including:
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#### **Complex biomolecular interactions**
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## Performance Metrics
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ESMFold2 was evaluated against state-of-the-art single-sequence and MSA-based structure prediction models on the FoldBench benchmark. ESMFold2 meets or exceeds performance by AlphaFold3 on antibody-antigen complex prediction, protein-protein complex prediction and [Runs N’ Poses](https://www.biorxiv.org/content/10.1101/2025.02.03.636309v1) benchmarks. For inference time-scaling on FoldBench, ESMFold2 scales gracefully with sample count, comparable to or exceeding AlphaFold3’s scaling behavior on the same targets.
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Refer to the [paper](https://biohub.ai/papers/esmc.pdf) for details on additional performance metrics.
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Many people on the Biohub AI Research team and prior EvolutionaryScale team contributed to the development of this model. It would not have been possible without them.
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