foldseek-analysis
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steineggerlab
Scripts to benchmark and train foldseek
Hello, I want to try reproduce your results for ./learnAlphabet.sh 20 100 data/pdbs_train.txt data/pdbs_val.txt out/ is it possible provide some intermediate data for comparison? log.txt, final round fasta, alignments scores,etc....
Hi @martin-steinegger and all the members, I found a outdated URL in the following code: ``` # Fetch PDBs if [ ! -d tmp/pdb ]; then curl https://wwwuser.gwdg.de/~compbiol/foldseek/scp40pdb.tar.gz | tar...
Per https://www.nature.com/articles/s41587-023-01773-0 Foldseek is GPLv3-licensed free open-source software. There is no license defined in this repository, is it also GPL version 3? In any case, I would appreciate if you...
@martin-steinegger When I use the following command: ./bench.fdr.noselfhit.awk scop_lookup.fix.tsv test.rocx to calculate the PR value for mmseqs2, the output is as shown in the figure; however, when calculating the PR...
 I have tried reproducing Supp. Fig. 5 using the scripts in this repository and also my own code but I get quite different results. For example, as shown in...
I have always had a doubt, or maybe I didn't read the paper very clearly I browsed through Wikipedia, but I still can't understand how the size of the p-value...
I have a question on how sensitivity is calculated in the SCOPe benchmark. In particular, it is on the total number of positives for the different cases: family, super-family, and...
I have always had a doubt, or maybe I didn't read the paper very clearly When searching on the web version, a 0-1 Probe will appear Value, how does this...
Hi the Foldseek Team: May I ask whether `./training/data/foldseek_v1/encoder.pt` is the final checkpoint? We find that the 3Di result from `./training/encode_pdbs.py` does not match that from the official Foldseek cpp...
