Issues

• tmalign/lolalign on master scale much worse than release 10 for many-query searches (per-query fork/join since 50011e2)

  steineggerlab/foldseek#614 · Filter by author ioChris opened on Nov 4, 2026

• uniprot hit annotations

  steineggerlab/foldseek#612 · Filter by author faylward opened on Oct 28, 2026

• Licensing of the 3Di encoder parameters redistributed under BSD-3-Clause in mini3di

  steineggerlab/foldseek#611 · Filter by author jinzomotsu opened on Oct 25, 2026
  1

• FoldSeek webserver multimer Lol-align failing

  steineggerlab/foldseek#610 · Filter by author wintherjonathan opened on Oct 23, 2026
  1

• Riboseek web server jobs failing

  steineggerlab/foldseek#609 · Filter by author AGrantUEA opened on Oct 5, 2026
  1

• Chains reported in interface alignments changes when query and target complexes are switched

  steineggerlab/foldseek#608 · Filter by author mcn3159 opened on Sep 22, 2026
  2

• Foldseek webserver search gives Conflicting TM-scores

  steineggerlab/foldseek#598 · Filter by author tjmier opened on Aug 3, 2026

• Jobs stuck in "pending", unable to rename subsequent files

  steineggerlab/foldseek#596 · Filter by author ojazzy16 opened on Jul 16, 2026
  1

• foldseek databases ESMAtlas30 ships a DB whose .lookup/header (_h) IDs don't match (same bug class as #465)

  steineggerlab/foldseek#593 · Filter by author ynishimuraLv opened on Jun 29, 2026

• Consulting about rate limits in the API usage

  steineggerlab/foldseek#591 · Filter by author joao13-vitoras opened on Jun 20, 2026

• very short proteins are skipped in foldseek easy-clsuter?

  steineggerlab/foldseek#589 · Filter by author Huilin-Li opened on Jun 14, 2026

• Discrepancy in structural search results due to database-size dependent E-value filtering

  steineggerlab/foldseek#585 · Filter by author luisbustom-oss opened on May 8, 2026

• easy-multimercluster crashes with munmap_chunk(): invalid pointer on mixed-chain-count inputs (regression after v10)

  steineggerlab/foldseek#584 · Filter by author bviggiano opened on May 7, 2026

• Creating a DB using ProstT5 and querying with a pdb file

  steineggerlab/foldseek#583 · Filter by author draperbarr opened on Apr 29, 2026

• Question about the exact pipeline & params used for AFDB v6 clustering

  steineggerlab/foldseek#582 · Filter by author yzy-pg opened on Apr 26, 2026

• conda version does not support interfacelddt as output field

  steineggerlab/foldseek#580 · Filter by author maven2306 opened on Apr 22, 2026

• Foldseek for pairwise structural alignment

  steineggerlab/foldseek#578 · Filter by author mohammadian-reza opened on Mar 22, 2026

• Why are the results so different between CPU and GPU?

  steineggerlab/foldseek#577 · Filter by author zhulab-yyf opened on Mar 22, 2026
  3

• --chainmap option for predefined chain-to-chain mapping of query and reference

  steineggerlab/foldseek#575 · Filter by author omgol411 opened on Mar 12, 2026

• Reduced hits in v9 vs v8 and AFDB50 download EOF error

  steineggerlab/foldseek#574 · Filter by author gioodm opened on Mar 10, 2026
  2

• output fasta of easy-cluster providing inconsistent sequences

  steineggerlab/foldseek#569 · Filter by author jmoojun opened on Mar 6, 2026

• easy-multimersearch returns empty results for homo-oligomeric complexes with chain count mismatch

  steineggerlab/foldseek#568 · Filter by author mf-rug opened on Mar 4, 2026

• Feature request: scrollable list view in HTML results for large queries

  steineggerlab/foldseek#566 · Filter by author dmoypal opened on Feb 12, 2026

• How to download the BFMD database?

  steineggerlab/foldseek#563 · Filter by author A4444z opened on Feb 3, 2026
  1

• Can Foldseek set a random seed?

  steineggerlab/foldseek#561 · Filter by author ruichaomao opened on Feb 3, 2026
  1