Release 2.3.0
Summary
This release adds support for the unknown residue X in query sequences, enabling MSA search on sequences containing ambiguous or unresolved amino acids.
New Features
Unknown Residue (X) Support
Query sequences may now contain the unknown residue character X, representing an ambiguous or unresolved amino acid.
- Accepted in all endpoints: Monomer, paired, and structural template search endpoints all accept
Xin query sequences. - No performance penalty: Search speed is equal to or faster than equivalent sequences without
X, since fewer hits survive prefiltering with degraded queries.
Refer to Unknown Residue (X) Tolerance for detailed benchmarks.
API Changes
Database Config Endpoint
Based on user feedback, the /biology/colabfold/msa-search/config/msa-database-configs endpoint will continue to be supported. However, all response fields except name and display_name are deprecated and should not be relied upon.
A new display_name field provides human-readable database names suitable for UI presentation (for example., UniProt Reference Clusters (30% identity) 2023-02). Display names can be customized using the NIM_MSA_DB_DISPLAY_NAMES environment variable or by mounting a custom /opt/nim/msa/config.py.
max_msa_sequences Validation
The API-level and GPU Server upper limits for max_msa_sequences have been unified into a single limit controlled by the existing NIM_GLOBAL_MAX_MSA_DEPTH environment variable (default 500). The OpenAPI specification now correctly reflects the effective upper bound. The redundant NIM_MSA_API_MAX_MSA_SEQUENCES variable has been removed. Most users are unaffected since GPU Server (enabled by default since 2.0.0) already enforced this limit.
Typed Response Schemas
The OpenAPI specification now includes proper return type schemas for the /biology/colabfold/msa-search/config/msa-database-configs endpoint (list[MSADataBaseConfig]) and the /biology/colabfold/msa-search/mmseqs2/version endpoint (MMSeqs2Version). Previously these endpoints did not have typed response schemas in the OpenAPI spec. This may affect clients using OpenAPI code generation tools.
API Version
The OpenAPI specification version has been updated from 1.2.0 to 1.3.0 to reflect new features, improved validation, and endpoint changes introduced in this release. This version bump signals to users and client tools that the API specification includes updates such as unknown residue support, changes to max_msa_sequences validation, and other adjustments described above.
Migration Notes
Model profile hashes have changed in this release. If you pin a specific profile using NIM_MODEL_PROFILE, update the hash. Run list-model-profiles to obtain the new hashes (refer to Listing Available Profiles for more information).