/alphafold3_evaluation

Primary LanguagePython

Download RNA IDs.

python download_rna_id.py

Release date is later than 9/30/2021. At least one RNA is included in the structure.

Download the information about these RNAs.

python download_rna_info.py

Information about the RNAs are saved in the rna_info.json file.

Download RNA cif files.

python download_cif.py

cif files rather than pdb file are downloaded because some RNAs have no pdb structure files.

Extract structures with only RNA.

python get_rna_only.py

Information about these RNA are saved in the rna_only.csv file.

Convert cif files to pdb files.

python cif2pdb.py rna_only.csv rna_only

Only the first model is retained. Chain names are reset from A-Z and then a-z. Residue numbers are reset from 1.

Run MC-Annotate

python annotate.py

Convert MC-Annotate output to dot-bracket form

python mc2db.py

Compile the Dataset

First, collect all the secondary structure information.

for i in $(cat in); do echo $i; cat rna_only/${i}.db; echo; done >rna_only.db

Next, compile the rna_only.db file by:

  1. Remove helices like (((((((())))))))
  2. Remove duplicates
  3. Remove structures like ..........

The compiled dataset for RNA-only prediction is the file rna_only_compiled.db.