Release Notes

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)