Skip to content

Foldseek 2-8bd520
Compare
Choose a tag to compare
@martin-steinegger martin-steinegger released this 08 Jul 16:32
· 1100 commits to master since this release
2-8bd520
8bd5201
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

Features

  • implemented reciprocal-best-structure-hit search (rbh and easy-rbh) similar to Monzon et al. preprint
  • C-alpha only structures are supported as input (backbone is completed using pulchra)
  • convertalis can output a HTML based result viz (--format-mode 3)
    Example: foldseek easy-search example/d1asha_ example/ aln.html tmp --format-mode 3

  • add support to read structures from tar and tar.gz in createdb, easy-search and easy-rbh.
    Example: foldseek easy-rbh UP000005640_9606_HUMAN_v2.tar UP000001940_6239_CAEEL_v2.tar rbh tmp --tar-include '.*pdb'
  • convertalis can output C-alpha, TMscore, TM rotation matrices (--format-output qca,tca,alntmscore,u,t respectively)
foldseek easy-search example/ example/ aln tmp --format-output query,target,alntmscore,u,t
cat aln
d2gdma_ d2gdma_ 1.000E+00       1.000,-0.000,0.000,0.000,1.000,0.000,-0.000,-0.000,1.000        -0.000,-0.000,0.000
d2gdma_ d1q1fa_ 7.971E-01       0.299,-0.746,-0.595,0.952,0.192,0.237,-0.062,-0.638,0.768       94.039,-63.738,34.804
d2gdma_ d1cqxa1 6.794E-01       0.694,-0.662,0.283,0.570,0.746,0.345,-0.439,-0.078,0.895        7.534,-93.168,-12.301
  • introduce --alt-ali to compute additional sub-optimal alignments for a query-target pairs #12
  • added Foldseek docker image (supports linux/amd64 and linux/arm64)

Bug fixes

  • fix invalid database type check in aln2tmscore #14
  • aln2tmscore could get stuck in an infinite loop #17
  • default sensitivity is now -s 9.5 and --max-seqs 1000
Assets 9
Loading