Predicts if a protein complex interface is biological or crystallographic.
Project description
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
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