Release 8-ef4e960 · steineggerlab/foldseek

At a glance: Added support for clustered, protein-complex searches (alpha-verison, feedback welcome) as well as improved HTML output.

Features

Implement easy-complex-search to find similar complexes structures in a database
Implement a cluster search --cluster-search 1, which speeds up searches through redundant databases. It first searches only the representatives and then expands the final alignment to all cluster members. Two downloadable DBs support this search: PDB and the Alphafold/UniProt50.
createclusearchdb allows to build a searchable cluster database (b4d7ec5)
convertalis HTML output updated to match search.foldseek.com output (96be67c)
Introduced Alphafold/UniProt50-minimal and updated cluster file downloads for regular Alphafold/UniProt50 to support cluster searches (93ad1d4, 2e9da41, daad5ab)
We added two modules scorecomplex and createcomplexreport to compute a TMscore between protein complex as well as to summarize the findings (938b591, a6c75cb)

Foldseek correctly computes coverage again (c63725d). Coverage computation was broken since release 6 (29979fb).
--alignment-type 0 (3Di-only) now correctly ignores amino-acid information (f0de872)
createdb could miss some files when recursively looking within directories on some file systems (d1d1b86)
convertalis --format-output can output qca or tca if only one of the two databases has C-alpha information (311845d)
--lddt-thr and --tmscore-thrare ignored when--sort-by-structure-bits 0` is set (b1b4710)

Much smaller precomputed index for --prefilter-mode 0 (exhaustive ungapped prefiltering) with --index-exclude 1 or --sort-by-structure-bits 0 (No C-alpha) with --index-exclude 2 or both with --index-exclude 3 (8f586c0)
Enabled WebAssembly (WASM) compilation for Foldseek (408cfae; pending on Daniel-Liu-c0deb0t/block-aligner#26)