Foldseek-Multimer

Foldseek-Multimer computes complex alignments from compatible chain-to-chain alignments by efficiently clustering their superposition vectors, enabling rapid and sensitive protein complex structure comparison at scale.

Key Features:

• High-speed alignment: Foldseek-Multimer achieves 3-4 orders of magnitude speedup compared to existing gold-standard methods while maintaining comparable alignment accuracy.
• Complex-pair comparison at scale: The tool can compare billions of complex-pairs in 11 hours.
• Chain-to-chain alignment clustering: Compatible chain-to-chain alignments are identified by efficiently clustering their superposition vectors.
• Open-source availability: The software is available as open-source code and through a webserver.

Scientific Applications:

• Protein complex structure alignment: Foldseek-Multimer aligns predicted and experimentally-determined protein complex structures to translate growing structural databases into biological discoveries.
• Large-scale complex database search: The tool enables comparison of massive collections of protein complex structures, including the BFMD database.

Methodology:

Foldseek-Multimer computes complex alignments from compatible chain-to-chain alignments, identified by efficiently clustering their superposition vectors.