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Building databases: PDB and AlphaFold

SnpEff supports Protein interactions calculated from PDB or AlphaFold. Adding protein interaction to existing SnpEff databases is rather involved, so it's recommended you use a pre-build database if available (e.g. human).

Requirements

In order to add protein data to a database, you need:

  • A SnpEff database for the organism. The database should have been built or downloaded prior to start adding the protein data
  • Protein data: One *.pdb.gz file for each protein. This can be downloaded from PDB (real data from cristalized proteins) or AlphaFold (predicted protein structures).
  • A "mapping file" that maps transcript IDs to protein IDs

Warning

Adding protein data to a SnpEff database, requires a database to be already built / downloaded

Protein structure data

You can download protein structure data from PDB by performing executing something like: 

rsync -rlpt -v -z --delete --port=33444 rsync.wwpdb.org::ftp_data/structures/divided/pdb/
See PDB's documentation.

For AlphaFold, you can download a tar file with all protein predictions from Ensembl's AlphaFold download page. Please check the documentation on how to cite AlphaFold if you use their databases in a paper.

PDB file filters: By default SnpEff will filter PDB files using the following criteria

  • SnpEff will search PDB formatted file in all subdirectories.
  • The file names must end with any of the extensions (case-sensitive): *.ent, *.ent.gz, *.pdb, or *.pdb.gz (as usual, files ending in .gz are expected to be gzip-compressed)
  • The protein ID must be parsed from the file name. Currently accepted file name formats are "PDB-style" (e.g. pdb7daa.ent.gz, where PDBID is 7daa) or AlphaFold-style (e.g. AF-Q9Y6V0-F9-model_v2.pdb.gz, where Uniprot-ID is Q9Y6V0)
  • The PDB file must have a resolution of at least 3 Angstrom. This value can be changed using the -res command line option

Info

If the PDB file has a missing resolution value, or the resolution is over 99.0, then it is assumed to be 'missing value' and not filtered. for instance, AlphaFold PDB files usually don't have resolution values since they are predictions, not measurements.

Mapping file

Since SnpEff uses trasncript ID information, whereas proteins use PDB IDs (or Uniprot IDs in case of AlphaFold), we need a file to map across these different IDs. You should provide a mapping file that maps transcriptId to proteinId:

The format is: tab-separated, one line per entry: 

transcriptID \t proteinID