Release Notes for NVIDIA NIM for OpenFold3#

Release 1.1.0#

Summary#

This release adds support for protein structural template inputs for complex structure prediction, and additional GPU hardware.

New Features#

Structural Template Support#

The NIM now accepts protein structural template inputs (single-chain) to guide structure prediction:

  • Template input: For each input, protein molecules can include structural templates in CIF format

  • Template guidance: Templates help constrain and improve structure predictions when experimental or predicted structures are available

  • Multiple templates: Each protein can have multiple structural templates

Additional GPU Support#

Support for additional NVIDIA GPU configurations:

  • NVIDIA B200: High-performance GPU for large-scale structure prediction

  • NVIDIA L40S: Cost-effective GPU option for production deployments

Telemetry Control#

Telemetry control: NIM Telemetry helps NVIDIA deliver a faster, more reliable experience with greater compatibility across a wide range of environments, while maintaining strict privacy protections and giving users full control.

Benefits:

  • Enhances performance and reliability: Provides anonymous system and NIM-level insights that help NVIDIA identify bottlenecks, tune performance across hardware configurations, and improve runtime stability.

  • Improves compatibility across deployments: Helps detect and resolve version, driver, and environment compatibility issues early, reducing friction across diverse infrastructure setups.

  • Accelerates troubleshooting and bug resolution: Allows NVIDIA to diagnose errors and regressions faster, leading to quicker support response times and higher overall availability.

  • Informs smarter optimizations and future releases: Real-world, aggregated telemetry data helps guide the optimization of NIM runtimes, model packaging, and deployment workflows, ensuring updates target the scenarios that matter most to users.

  • Protects user privacy and data security: Collects only minimal, anonymous metadata, such as hardware type and NIM version. No user data, input sequences, or prediction results are collected.

  • Fully optional and configurable: Telemetry collection is disabled by default. You can toggle telemetry at any time using environment variables.

Configuration:

  • Set NIM_TELEMETRY_MODE=0 to disable telemetry (default)

  • Set NIM_TELEMETRY_MODE=1 to enable telemetry

For more information about data privacy, what is collected, and how to configure telemetry, refer to:

Supported Features#

All features from release 1.0.0 remain supported, with the addition of structural templates for protein molecules.

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)