> This page is for MSA Search, version 2.1.0.
> For other versions, use one of these documentation indexes:
> - 2.6.0 (Latest) (default): https://docs.nvidia.com/nim/bionemo/msa-search/2.6.0/llms.txt
> - 2.5.0: https://docs.nvidia.com/nim/bionemo/msa-search/2.5.0/llms.txt
> - 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 2.1.0

### Summary

This release introduces Paired MSA Search for protein complexes (multimers), enabling accurate co-evolutionary analysis across multiple chains. Paired search is now a first-class feature with its own API endpoint.

### Key Changes

#### Paired MSA Search for Protein Complexes

A new endpoint `/biology/colabfold/msa-search/paired/predict` enables paired MSA search for protein complexes:

* **Multi-chain input**: Submit multiple protein sequences (one per chain) in a single request
* **Species-based pairing**: Homologous sequences are paired by species across chains, preserving co-evolutionary signals essential for accurate complex structure prediction
* **Pairing strategies**: Choose between "greedy" (maximize coverage) or "complete" (require all chains) pairing modes
* **Flexible output**: Return per-chain alignments or raw combined output via the `unpack` parameter

This feature is essential for accurate structure prediction of protein complexes using tools like AlphaFold-Multimer, Boltz, and similar methods.

#### API Changes

* **New endpoint**: `/biology/colabfold/msa-search/paired/predict` for paired/multimer MSA search

* **New parameters for paired search**:

  * `sequences`: List of protein sequences (one per chain)
  * `pairing_strategy`: Cross-chain pairing mode ("greedy" or "complete")
  * `unpack`: Control output format (per-chain or combined)

* **Output format**: Paired search always returns A3M format

### New Features and Improvements

* Paired MSA search for protein complexes with 2+ chains
* Support for greedy and complete pairing strategies
* Per-chain or combined alignment output options
* Improved API documentation and examples