> This page is for OpenFold3, version 1.2.0.
> For other versions, use one of these documentation indexes:
> - 1.6.0 (Latest) (default): https://docs.nvidia.com/nim/bionemo/openfold3/1.6.0/llms.txt
> - 1.5.0: https://docs.nvidia.com/nim/bionemo/openfold3/1.5.0/llms.txt
> - 1.4.0: https://docs.nvidia.com/nim/bionemo/openfold3/1.4.0/llms.txt
> - 1.3.0: https://docs.nvidia.com/nim/bionemo/openfold3/1.3.0/llms.txt
> - 1.2.0: https://docs.nvidia.com/nim/bionemo/openfold3/1.2.0/llms.txt
> - 1.1.0: https://docs.nvidia.com/nim/bionemo/openfold3/1.1.0/llms.txt
> - 1.0.0: https://docs.nvidia.com/nim/bionemo/openfold3/1.0.0/llms.txt

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> For a complete documentation index, see https://docs.nvidia.com/nim/bionemo/llms.txt.
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## Release 1.0.0

### Summary

This is the first release of NVIDIA NIM for OpenFold3.

### Supported Features

#### Entity Types

The NIM request API accepts the following molecular entity types:

* **Protein**: Amino acid sequences
* **DNA**: DNA sequences
* **RNA**: RNA sequences
* **Ligand**: Small molecules specified via CCD codes or SMILES strings

#### Multiple Entities and Complexes

The API accepts inputs with multiple entities across multiple types, enabling
prediction of complex biomolecular structures. For example:

* Monomeric proteins: 1 protein sequence
* Protein-ligand complexes: 1 or more protein sequences, 1 or more ligands
* Homomeric protein complexes: 2 or more identical protein sequences
* Heteromeric protein complexes: 2 or more nonidentical protein sequences
* Protein-DNA complexes: 1 or more protein sequences, 1 or more DNA sequences
* Protein-RNA complexes: 1 or more protein sequences, 1 or more RNA sequences

#### Multiple Sequence Alignment (MSA) Support

The NIM accepts MSA inputs with flexible configuration:

* **MSA Requirements**: MSA inputs are required for protein and RNA entity types
* **Format support**: Multiple alignment file formats are supported:
  * `a3m` : A3M format
  * `csv` : CSV format
* **MSA types**:
  * Unpaired MSAs for protein sequences and RNA sequences.
  * Paired MSAs for inputs with multiple non-identical protein sequences.

Note: The OpenFold3 NIM accepts paired MSA inputs, but does **not** perform 'online' pairing of MSAs.

#### Inference Parameters

**Forward Pass Parameters:**

* `diffusion_samples`: Number of independent structures to generate (1-5, default: 1)

#### Structure Templates

* **Note**: This release does not support structure template inputs. Predictions are generated without template guidance.

#### Output Formats

* **CIF**: Crystallographic Information File format (supported)
* **PDB**: Protein Data Bank format (supported)
* **mmCIF**: Macromolecular CIF format (not yet supported)