search

steineggerlab / foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.
https://foldseek.com
GNU General Public License v3.0
693 stars 91 forks source link

Comparison of specified structure fragments #263

Open huizhen2014 opened 2 months ago

huizhen2014 commented 2 months ago

Wonderful software, thanks a lot.

I want to the all-in-all search like EFI - Enzyme Similarity Tool function. I found when I took one query for easy-search in uniprot database, I will get thousands hits with different alignment location (from start to end aa). Then, I want do a further separation for theses hits, and I believe If I can extract these aligned structure for each hits to do further all-in-all search. I will get more precise separation for the secondary all-in-all search, which will be enough to point out there cognate substrates. The aligned structure fragments I want to extract for further search: image

The flow is below:

  1. search homologous structure, and get hits
  2. extract the aligned fragments (fragmented structure) to get the confined hits
  3. all-in-all search for the confined hits ( which will hope to figure out the relationship between conserved structure and cognate substrate.

Thanks a lot, or there are alternative methods could help me solve this analysis thought.

huizhen2014 commented 2 months ago

Sorry， here is my scripts: foldseek easy-search 7MDC.pdb ../foldseek_database/uniprot 7mdc_uniprot_0.9 7mdc_uniport_0.9_tmp --exhaustive-search 1 --cov-mode 2 --format-output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,prob,lddt,alntmscore,taxid,taxname,taxlineage -e 0.001 -c 0.9 version: foldseek Version: f629bbe108595ebf0886dd6974e9959a4d962af3