Release Notes for NVIDIA NIM for OpenFold3#

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)