How a virtual amino acid is represented in 3Di Sequence?

steineggerlab / foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

https://foldseek.com

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How a virtual amino acid is represented in 3Di Sequence? #186

Open suresh-pokharel opened 9 months ago

suresh-pokharel commented 9 months ago

I have some protein sequences that contain virtual amino acids, i.e. X. When I convert them to 3Di sequence, it looks like it discards the virtual amino acids which leads to different lengths of AA sequence and 3Di Sequence.

I am using these commands to convert to 3Di:

foldseek createdb pdb_files/selected_prediction.pdb DB
foldseek lndb DB_h DB_ss_h
foldseek convert2fasta DB_ss DB_ss.fasta