clustering of multimers

[adrienchaton]

Hello,

I am trying to cluster pdbs with several chains, in this case they are all dimers (antibodies).

I have not found whether or not foldseek would allow that but since I could run latest foldseek version on a folder with monomers, I guess the issue I am encountering now is related to limitations of the algorithm to work on single chains only ?

foldseek createdb ./pdbs DB this one works fine but at the second step to call foldseek search then I get an error

k-mer similarity threshold: 78
Starting prefiltering scores calculation (step 1 of 1)
Query db start 1 to 2531172
Target db start 1 to 2531172
Segmentation fault (core dumped)                                  ] 0.00% 1 eta -
Error: Kmer matching step died

Is there a procedure to cluster dimers with FoldSeek please ? Since I will work with antibodies, it is fine for me to assume all the pdbs have the same number of chain = 2.

Thanks!

[martin-steinegger]

Currently this is not supported. We are working on this.

[adrienchaton]

thanks for your reply and the good job done! that will be a great addition to this tool

[adrienchaton]

one thought I had, could anything related to the glycine linker trick as in e.g. AF multimer, be applicable to FoldSeek?

[edumenezes77]

I'm working on the same

I tried to do a clustering of antibodies based on the orientation of the VH/VL domains.

And I had to designate the same chains id of both as one (I treated H and L chains as A) and I renumbered the residues so as not to have overlapping numbers.

[sirius777coder]

Hi, have you tried this linker or other tools in dimer structure clustering? I have meet the same issue