PRODIGY-cryst

Collection of scripts to predict whether an interface in a protein-protein complex is biological or crystallographic from its atomic coordinates.

Installation

pip install prodigy-cryst

Usage

Type --help to get a list of all the possible options.

$ prodigy_cryst --help
usage: prodigy_cryst [-h] [--contact_list] [-q] [--selection A B [A,B C ...]] structf

Biological/crystallographic interface classifier based on Intermolecular Contacts (ICs).

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

optional arguments:
  -h, --help            show this help message and exit
  --contact_list        Output a list of contacts
  -q, --quiet           Outputs only the predicted interface class

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 ...]

Examples

Download PDB file 1ppe from the PDB and run the script on it.

wget https://files.rcsb.org/download/1PPE.pdb

Check how PRODIGY-cryst works on the 1PPE.pdb file. The script will output the number of intermolecular contacts, the number of contacts of each type, the link density, and the predicted interface class.

$ prodigy_cryst 1PPE.pdb
[+] Reading structure file: /home/rodrigo/1PPE.pdb
[+] Selection: E, I
[+] No. of intermolecular contacts: 71
[+] No. of charged-charged contacts: 4
[+] No. of charged-polar contacts: 8
[+] No. of charged-apolar contacts: 24
[+] No. of polar-polar contacts: 0
[+] No. of apolar-polar contacts: 15
[+] No. of apolar-apolar contacts: 20
[+] Link density: 0.14
[+] Class: BIO 0.804 0.196