mcguffin/modfold4 repository overview

Setup:

1. Download the database file (this file will be updated every week, eventually): http://www.reading.ac.uk/bioinf/downloads/ModFOLD4_db.tar.bz2⁠
2. bunzip2 ModFOLD4_db.tar.bz2
3. tar xf ModFOLD4_db.tar

Set database & io paths in your shell (optional, alternatively include the full paths when you run):

1. export MF4_DB=/location/of/your/database/directory/
2. export MF4_IN=/location/of/your/input/files/
3. export MF4_OUT=/location/for/ModFOLD4/output/

Run with a single model file in PDB format: docker run -v $MF4_DB:/home/Liam/data/ -v $MF4_IN:/home/Liam/ModFOLD4_input/ -v $MF4_OUT:/home/Liam/ModFOLD4_output/ mcguffin/modfold4 <seqres.fasta> <input.pdb>

Run with gzipped tar file containing a directory of models for the same sequence: docker run -v $MF4_DB:/home/Liam/data/ -v $MF4_IN:/home/Liam/ModFOLD4_input/ -v $MF4_OUT:/home/Liam/ModFOLD4_output/ mcguffin/modfold4 <seqres.fasta> <input.tar.gz>

Note: results will be cached and jobs will run much more quickly if models with the same sequence have been evaluated before, the same output directory is used and the cached results are less than a week old.