Martin Steinegger

Yes, please check `pdb100_clu`. You can convert it to a human-readable file using the following command. ``` foldseek createtsv pdb100 pdb100 pdb100_clu pdb100_clu.tsv ``` The first column is the representative...

You need to add the `prob` as output fields. What you see in the third column is the sequence identity. In default we show the following fields: `query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits`. You can...

Okay, we should now have a proper pdb100 where everything should work. In order to use it please update foldseek and re-download the PDB. Sorry for the delay, it took...

We are correcting scores by subtracting a reverse score (alignment score with inverted query) as a compositional bias correction. This can result in negative scores.

We always consider the database or collection size for computing the e-value.

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

We utilize mmap for reading our ss database in prefilter mode 1. During this process, every page is brought into memory, but the system has the capability to eliminate pages...

@YTang906 we now implemented https://github.com/steineggerlab/foldseek/commit/f0de872f3ab84bbd5c173424a6633f0384f3adbd the 3Di only mode better. You could give it a try now.

We do not store the full PDB in our databases but just C𝛼 to keep the databases small. In order to get the full PDB files you would need to...

Neither of these databases is clustered by `foldseek easy-cluster`. We only provide databases clustered by amino acid sequence. The only preclustered databases are Alphafold/UniProt50, PDB and ESMAtlas30 were clustered through...