isopeptor 0.0.73

Package for isopeptide bond prediction and analysis based on pyjess

ISOPEPtide bond detecTOR

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.

Installation

pip install isopeptor

Usage

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        	0.987      	A    	590    	636  	729    	LYS         	ASP       	ASN         	CnaA-like	0.0  	0.004	8beg_A_590_636_729   
8beg        	0.987      	A    	756    	806  	894    	LYS         	ASP       	ASN         	CnaA-like	0.0  	0.028	8beg_A_756_806_894   
8beg        	0.987      	A    	922    	973  	1049   	LYS         	ASP       	ASN         	CnaA-like	0.0  	0.015	8beg_A_922_973_1049  
8beg        	0.987      	A    	1076   	1123 	1211   	LYS         	ASP       	ASN         	CnaA-like	0.0  	0.015	8beg_A_1076_1123_1211
7woi        	0.987      	A    	57     	158  	195    	LYS         	GLU       	ASN         	CnaB-like	0.001	0.019	7woi_A_57_158_195    
7woi        	0.987      	A    	203    	246  	318    	LYS         	ASP       	ASN         	CnaA-like	0.0  	0.012	7woi_A_203_246_318   
5dz9        	0.987      	A    	556    	606  	703    	LYS         	ASP       	ASN         	CnaA-like	0.0  	0.009	4z1p_A_3_53_150      
5dz9        	0.987      	A    	730    	776  	861    	LYS         	ASP       	ASN         	CnaA-like	0.0  	0.019	4z1p_A_177_223_308   
4z1p        	0.987      	A    	3      	53   	150    	LYS         	ASP       	ASN         	CnaA-like	0.0  	0.009	4z1p_A_3_53_150      
4z1p        	0.987      	A    	177    	223  	308    	LYS         	ASP       	ASN         	CnaA-like	0.0  	0.019	4z1p_A_177_223_308   
6to1_af     	0.505      	A    	13     	334  	420    	LYS         	ASP       	ASN         	CnaA-like	0.548	0.002	4uzg_A_187_225_330

To redirect the output to a .tsv file use:

isopeptor tests/data/test_structures/ > output.tsv

Full command line options:

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.

Test

python -m unittest discover -s tests -p "test_isopeptide.py"