easy-search hangs on scop40 test

[rcedgar]

I'm trying to implement the SCOP40 test using the latest foldseek. The creatdb command completes; the easy-search command runs for a while but then hangs indefinitely. Advice welcomed for how to implement this in the best way for measuring foldseek speed and accuracy, thanks for any help!

# foldseek Version: 915ef7ddce1bd77080208eff8a434c0985ae7492

foldseek createdb \
  ../scop40pdb/pdb \
  scop40

/bin/time -v -o foldseek.time \
foldseek easy-search \
  ../scop40pdb/pdb \
  scop40 /
  --format-output "query,target,pident,evalue,alntmscore" \
  hits.txt

[rcedgar]

Update -- I was able to work around the problem by removing alntmscore from the format-output option, I'm guessing computing the TM alignment is much slower than the S-W 3Di alignment and is not needed to calculate the E-value.

[12047019]

I want to know where you got the SCOP40 or 35 files to createdb? I have to do the SCOP against my bundles of protein structures but couldn't get the files to createdb.

[rcedgar]

https://wwwuser.gwdg.de/~compbiol/foldseek

[martin-steinegger]

I am not recommending to use this, it’s quite an old version. It make sense to use the latest for annotation or benchmarking https://scop.berkeley.edu/

[rcedgar]

Noted thanks, will do for anything written up but for preliminary work it's helpful that the expensive computes for DALI and TMalign are included in the downloads for the foldseek paper.

[12047019]

Thanks @rcedgar @martin-steinegger, got it. It would be so kind of you if you preassemble and add it like other databases in the foldseek @martin-steinegger

[rcedgar]

Hi @martin-steinegger with --format-output "query,target,evalue" foldseek completes SCOP40 quickly but the sensitivity is lower than reported in the paper. Presumably I need to tweak some options such as --max-seqs and --exhaustive-search but I don't see the command line in Methods or Supp Data, What are recommended options for comparative validation? Thanks!

[martin-steinegger]

We have all scripts for benchmarking here https://github.com/steineggerlab/foldseek-analysis

[rcedgar]

Much better! Seems accuracy is getting close to DALI now, is there any explanation of improvements in the algorithm?