> This page is for MSA Search, version 2.5.0.
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> - 2.4.0: https://docs.nvidia.com/nim/bionemo/msa-search/2.4.0/llms.txt
> - 2.3.0: https://docs.nvidia.com/nim/bionemo/msa-search/2.3.0/llms.txt
> - 2.2.0: https://docs.nvidia.com/nim/bionemo/msa-search/2.2.0/llms.txt
> - 2.1.0: https://docs.nvidia.com/nim/bionemo/msa-search/2.1.0/llms.txt
> - 2.0.0: https://docs.nvidia.com/nim/bionemo/msa-search/2.0.0/llms.txt
> - 1.0.0: https://docs.nvidia.com/nim/bionemo/msa-search/1.0.0/llms.txt

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## Release 2.2.0

### Summary

This release introduces a dedicated Structural Template Search endpoint for finding homologous protein structures, case-insensitive database name matching, along with bug fixes and documentation improvements.

### New Features

#### Structural Template Search

A new Structural Template Search feature enables template search for protein structure prediction:

* **Template discovery**: Search PDB70 and/or PDB100 and other structural databases to find proteins with similar structures to your query sequence
* **Structure retrieval**: Automatically retrieve mmCIF files for the top template hits
* **Combined MSA output**: Returns both structural templates and MSA alignments in a single request
* **Flexible database selection**: Choose which structural databases to search and which sequence databases to use for MSA generation

This feature is essential for template-based protein structure prediction methods.

#### Case-Insensitive Database Names

Database names are now matched case-insensitively across all endpoints. You can specify database names in any case (for example, `uniref30_2302`, `Uniref30_2302`, or `UNIREF30_2302`) and the API will find the correct database. The response preserves the exact case you specified in the request.

This change simplifies API usage by eliminating case-sensitivity errors and provides flexibility in how database names are specified.

**Note on `["all"]` database resolution**: When using `databases: ["all"]` (or not specifying MSA databases), the response currently uses display names configured via `NIM_MSA_DB_NAME_MAPPINGS` (for example, `Uniref30_2302`, `PDB70_220313`) for backwards compatibility. **In MSA 3.0, `["all"]` will resolve to all-lowercase names** (for example, `uniref30_2302`, `pdb70_220313`). If your code parses database names from responses, we recommend using case-insensitive comparisons to ensure forward compatibility.

### Bug Fixes

#### Consistent Profile Generation Database Selection

Fixed an issue where the database used for profile generation depended on filesystem path ordering when using `["all"]` for database selection. The fix ensures the configured default database for profile generation (uniref30_2302 by default) is always used when available, regardless of filesystem ordering.

#### Merged Alignment Now Includes All Requested Databases

Fixed an issue where the merged "colabfold" alignment output only included results from expandable databases. Doing so omits results from non-expandable databases (like pdb70_220313) even when those were explicitly requested.

Previously, if a user requested `databases: ["uniref30_2302", "pdb70_220313"]`, all databases were searched but only expandable database results were merged into the combined "colabfold" output. The fix ensures all requested database results are included in the merged alignment, better matching user expectations and providing a more intuitive result.

### Documentation

* Added [Task-Specific Profiles and Custom Databases](/nim/bionemo/msa-search/2.5.0/task-specific-profiles-and-custom-databases) guide covering database profiles for reduced storage, custom database configuration, and manually downloading individual databases from NGC.
* Added [Indexing Databases for GPU Server](/nim/bionemo/msa-search/2.5.0/indexing-databases-for-gpu-server) guide for users who need to index custom or third-party databases for GPU Server support.
* Added [Observability](/nim/bionemo/msa-search/2.5.0/observability) guide covering metrics and telemetry configuration. Telemetry is disabled by default and can be enabled through `NIM_TELEMETRY_MODE`.

### Deprecations

* **`/biology/colabfold/msa-search/config/msa-database-configs` endpoint**: This endpoint is deprecated in favor of `/v1/metadata` and will be removed in MSA 3.0. Use `/v1/metadata` to retrieve information about available databases and model profiles.

### Migration Notes

No migration steps required.