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 ...]

prodigy 2.1.3                                     December 2023                                       PRODIGY(1)