PDBbind Database



In [1]:

    
from __future__ import print_function, division, unicode_literals

import oddt
from oddt.datasets import pdbbind

oddt.toolkit.image_size = (400, 400)

print(oddt.__version__)









    



0.4.1-16-gb8cc8d0

Download a dataset from PDBbind and unpack (I used core-set 2016).



In [2]:

    
%%bash
wget -qO- http://www.pdbbind.org.cn/download/pdbbind_v2016_core.tar.gz | tar xz



In [3]:

    
directory = './core-set/'

We will use the pdbbind class.



In [4]:

    
pdbbind_database = pdbbind(home=directory, 
    version='2016', 
    default_set='core') # Available sets in wrapper: core, refined, general_PL (general for 2007)

You can get one target or iterate over all of them. To do it you can use PDB ID of a target or an index from list in INDEX file (INDEX_refined_data.2016).

The class has two properties: ids and activities.



In [5]:

    
all_ids = pdbbind_database.ids
print('Number of targets:', len(all_ids))
print('First ten targets:', all_ids[:10])









    



Number of targets: 290
First ten targets: ['3ao4', '3gv9', '1uto', '1ps3', '4ddk', '4jsz', '3g2z', '3dxg', '3l7b', '3gr2']



In [6]:

    
all_activities = pdbbind_database.activities
print('First ten activities:', all_activities[:10])









    



First ten activities: [2.07, 2.12, 2.27, 2.28, 2.29, 2.3, 2.36, 2.4, 2.4, 2.52]

Let's choose one target.



In [7]:

    
target = pdbbind_database[0]

You can always check PDB ID.



In [8]:

    
target.id









    Out[8]:





'3ao4'

Target has three properties: protein, pocket and ligand. All of them are of oddt.tolkit.Molecule class.

Let's find the largest ligand.



In [9]:

    
max_atoms = 0

for target in pdbbind_database:
    if max_atoms < len(target.ligand.atoms):
        max_atoms = len(target.ligand.atoms)
        largest = target

print('Target ID:', largest.id, '\nNumber of atoms:', max_atoms)









    



Target ID: 3ag9 
Number of atoms: 140



In [10]:

    
largest_ligand = largest.ligand
largest_ligand.removeh()
largest_ligand









    Out[10]:

If you want to check activity, you can use the sets dict.



In [11]:

    
pdbbind_database.sets['core'][largest.id]









    Out[11]:





8.05