Python package for the detection of intamolecular isopeptide bonds in protein structures. The method is described in "Isopeptor: a tool for detecting intramolecular isopeptide bonds in protein structures".
Isopeptor can be accessed via this google colab or installed and run locally.
Read the documentation for complete information on its usage and examples.
pip install isopeptor
From the command line:
isopeptor tests/data/test_structures/
Output:
protein_name probability chain r1_bond r_cat r2_bond r1_bond_name r_cat_name r2_bond_name bond_type rmsd r_asa template
8beg 0.991 A 590 636 729 LYS ASP ASN CnaA-like 0.0 0.1 8beg_A_590_636_729
8beg 0.991 A 756 806 894 LYS ASP ASN CnaA-like 0.0 0.1 8beg_A_756_806_894
8beg 0.991 A 922 973 1049 LYS ASP ASN CnaA-like 0.0 0.1 8beg_A_922_973_1049
8beg 0.991 A 1076 1123 1211 LYS ASP ASN CnaA-like 0.0 0.1 8beg_A_1076_1123_1211
5dz9 0.991 A 556 606 703 LYS ASP ASN CnaA-like 0.0 0.1 4z1p_A_3_53_150
5dz9 0.991 A 730 776 861 LYS ASP ASN CnaA-like 0.0 0.1 4z1p_A_177_223_308
4z1p 0.991 A 3 53 150 LYS ASP ASN CnaA-like 0.0 0.1 4z1p_A_3_53_150
4z1p 0.991 A 177 223 308 LYS ASP ASN CnaA-like 0.0 0.1 4z1p_A_177_223_308
7woi 0.909 B 57 158 195 LYS GLU ASN CnaB-like 0.314 0.1 5j4m_A_47_139_172
1amx 0.882 A 176 209 293 LYS ASP ASN CnaA-like 0.353 0.1 2f68_X_176_209_293
7woi 0.875 A 203 246 318 LYS ASP ASN CnaA-like 0.363 0.1 4hss_A_187_224_299
7woi 0.838 B 355 435 466 LYS GLU ASN CnaB-like 0.403 0.1 8f70_A_299_386_437
6to1_af 0.607 A 13 334 420 LYS ASP ASN CnaA-like 0.565 0.1 5mkc_A_191_600_695
To redirect the output to a .tsv file use:
isopeptor tests/data/test_structures/ > output.tsv
usage: isopeptor [-h] [--distance DISTANCE] [--fixed_r_asa FIXED_R_ASA] [--eval_geometry] path_to_structure_files
Run isopeptide bond prediction from command line. Usage: isopeptor path/to pdb files/ > isopeptide_bonds.csv
positional arguments:
path_to_structure_files
Path to directory containing .pdb/.cif files.
options:
-h, --help show this help message and exit
--distance DISTANCE Specifies permissivity of jess search. The higher, the more permissive.
--fixed_r_asa FIXED_R_ASA
Fixes the relative solvent accessible area using a value between 0 and 1 to speed up the prediction.
--eval_geometry Run geometric evaluation of isopeptide bonds.
python -m unittest discover -s tests -p "test_isopeptide.py"
If you use isopeptor please cite:
@article {Costa2024.12.24.630248,
author = {Costa, Francesco and Barringer, Rob and Riziotis, Ioannis and Andreeva, Antonina and Bateman, Alex},
title = {Isopeptor: a tool for detecting intramolecular isopeptide bonds in protein structures},
elocation-id = {2024.12.24.630248},
year = {2024},
doi = {10.1101/2024.12.24.630248},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2024/12/25/2024.12.24.630248},
eprint = {https://www.biorxiv.org/content/early/2024/12/25/2024.12.24.630248.full.pdf},
journal = {bioRxiv}
}