---
name: "prodigy"
section: "1"
platform: "linux"
package: "python3-prodigy"
version: "2.2.5-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/prodigy"
---

# prodigy(1)

binding affinity predictor

## NAME

prodigy - binding affinity predictor

## DESCRIPTION

usage: prodigy \[-h\] \[--distance-cutoff DISTANCE\_CUTOFF\]

-

  \[--acc-threshold ACC\_THRESHOLD\] \[--temperature TEMPERATURE\] \[--contact\_list\] \[--pymol\_selection\] \[-q\] \[--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

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 \[A,B C ...\]