Foldseek is a fast and sensitive command-line tool for comparing large protein structure datasets.
It supports monomer and multimer searches as well as structural clustering. Foldseek runs on CPUs and offers optional GPU acceleration.
This is free and open source software.
Key Features
- Searches large protein structure collections.
- Supports monomer and multimer structure searches.
- Clusters proteins using structural alignment.
- Accepts PDB, mmCIF and FASTA input.
- Searches PDB, AlphaFoldDB, ESMAtlas and custom databases.
- Offers optional NVIDIA GPU acceleration.
- Uses the ProstT5 language model to compare protein sequences without requiring predicted structures.
- Offers local, global and multi-domain alignment modes.
- Produces tab-separated data, superimposed PDB files and interactive HTML reports.
- Provides precompiled Linux builds for x86-64 and ARM64 systems.
Website: github.com/steineggerlab/foldseek
Support:
Developer: Steinegger Lab
License: GNU General Public License v3.0
Foldseek is written in C and C++. Learn C with our recommended free books and free tutorials. Learn C++ with our recommended free books and free tutorials.
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