Skip to navigation

Release Notes

December 15, 2025

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