NAME

       prodigy - binding affinity predictor

DESCRIPTION

       usage: prodigy [-h] [--distance-cutoff DISTANCE_CUTOFF]

              [--acc-threshold   ACC_THRESHOLD]   [--temperature   TEMPERATURE]  [--contact_list]
              [--pymol_selection] [-q] [-V] [--selection A B [A,B C ...]]  structf

       Binding affinity predictor based on Intermolecular Contacts (ICs).

       Anna Vangone and Alexandre M.J.J. Bonvin, Contacts-based prediction of binding affinity in
       protein-protein complexes.  eLife (2015)

   positional arguments:
       structf
              Structure to analyse in PDB or mmCIF format

   options:
       -h, --help
              show this help message and exit

       --distance-cutoff DISTANCE_CUTOFF
              Distance cutoff to calculate ICs

       --acc-threshold ACC_THRESHOLD
              Accessibility threshold for BSA analysis

       --temperature TEMPERATURE
              Temperature (C) for Kd prediction

       --contact_list
              Output a list of contacts

       --pymol_selection
              Output a script to highlight the interface (pymol)

       -q, --quiet
              Outputs only the predicted affinity value

       -V, --version
              Print the version and exit.

       Selection Options:

              By  default,  all  intermolecular contacts are taken into consideration, a molecule
              being defined  as  an  isolated  group  of  amino  acids  sharing  a  common  chain
              identifier.  In specific cases, for example antibody-antigen complexes, some chains
              should be considered as a single molecule.

              Use the --selection  option  to  provide  collections  of  chains  that  should  be
              considered  for  the  calculation.  Separate  by  a space the chains that are to be
              considered _different_ molecules. Use commas to include multiple chains as part  of
              a single group:

       --selection A B => Contacts calculated (only) between chains A and B.

       --selection A,B C => Contacts calculated (only) between chains A and C; and B and C.

       --selection A B C => Contacts calculated (only) between chains A and B; B and C; and A and
              C.

       --selection A B [A,B C ...]