Foldseek Release 10-941cd33

Foldseek Release 10

Foldseek introduces GPU support for monomer and multimer search, improved profile search and ProstT5 integration, new databases, several performance improvements and bug fixes.

Major Features

• GPU Support for Search and Multimers
  Both easy-search and easy-multimersearch now support accelerated searches on the GPU execution. Use --gpu 1 to enable GPU mode and CUDA_VISIBLE_DEVICES to control the number of GPUs. (#391, #411). GPU-enabled binaries require glibc >= 2.17, NVIDIA driver >= 525.60.13, and a Turing or newer GPU. On a single 4090 GPU, searches are 4x faster, and on eight GPUs, they are up to 37x faster than a 128-core CPU using the k-mer prefilter. For more details, see our preprint.
• Improved Structural Profile Search
  Alignment results can now be converted into position-specific scoring profiles with result2profile, enabling the creation of structural protein family representations. (#411)
• Enhanced ProstT5 Integration
  Multi-GPU and Apple Metal support added, Improved handling of large input sequence through splitting and switched backend to llama.cpp for better compatibility and performance. (#391)
• New Databases
  Introduced BFVD as a new virus-specific Foldseek database. (#344).
  For more details about the database, check out the BFVD paper.
• Improved Multimer Search Workflows
  Optimized multimer workflows for improved speed and reliability, with contributions by @Woosub-Kim. For more details, see our Foldseek-Multimer preprint.
• Clustering Multimers (First Version)
  Introduced experimental multimer clustering (easy-multimercluster) by @sooyoung-cha and @rachelse, supporting clustering by interface LDDT, chain TM-score, and complex coverage. See filtercomplex for more details.

Breaking Changes

• Results may differ as masking of letters repeated six or more times is now enabled by default --mask-n-repeat. Disable this option to reproduce previous results.

Other Features

• Improved Compatibility with MMseqs2 Modules: createsubdb, makepaddedseqdb, and result2profile now work seamlessly with Foldseek databases.
• Taxonomy Reports in easy-search: Added options to generate taxonomy reports directly within easy-search. (#389)
• Residue Mapping Rework: Residue mapping has been reworked to combine most gemmi amino acids with previous Foldseek amino acids. (#387)

Bug Fixes

• Fix order dependent --format-output issue of qtmaln,ttmaln,lddt,u,t (b40729c)
• Fix clustering of structures without Cα information (0d8d966)

Full Changelog

View the full changelog: 9-427df8a...10-941cd33.