You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
To whom it may concern,
I want to reproduce the report of a paper https://www.biorxiv.org/content/10.1101/2020.03.22.002386v1. In this paper, the authors find 322 proteins that interact with SARS-CoV-2 and find the drugs that related to these proteins. I already download the Uniprot ID for each of these proteins, and I have converted them to CHEMBL ID. Now I have a list file of CHEMBL ID that represents proteins, I want to find all phase 4 drugs that interact with these proteins. The following is my code.
from chembl_webresource_client.new_client import new_client
chembl_id = []
with open("chembd_list_human.txt", "r") as fopen:
lines = fopen.readlines()
for line in lines:
chembl_id.append(line.split()[0])
#chembl_id = ['CHEMBL1163125', 'CHEMBL2095186']
for node in chembl_id:
activities = new_client.mechanism.filter(target_chembl_id=node)
compound_ids = [x['molecule_chembl_id'] for x in activities]
approved_drugs = new_client.molecule.filter(molecule_chembl_id__in=compound_ids).filter(max_phase=4)
for drug in approved_drugs:
for key, value in drug.items():
if key=='molecule_chembl_id':
print(value)
However, from this code I only get a very little subset of the results that the paper represented. Could anyone give any suggestions how to get a better search strategy?
Best wishes,
The text was updated successfully, but these errors were encountered:
To whom it may concern,
I want to reproduce the report of a paper https://www.biorxiv.org/content/10.1101/2020.03.22.002386v1. In this paper, the authors find 322 proteins that interact with SARS-CoV-2 and find the drugs that related to these proteins. I already download the Uniprot ID for each of these proteins, and I have converted them to CHEMBL ID. Now I have a list file of CHEMBL ID that represents proteins, I want to find all phase 4 drugs that interact with these proteins. The following is my code.
from chembl_webresource_client.new_client import new_client
chembl_id = []
with open("chembd_list_human.txt", "r") as fopen:
lines = fopen.readlines()
for line in lines:
chembl_id.append(line.split()[0])
#chembl_id = ['CHEMBL1163125', 'CHEMBL2095186']
for node in chembl_id:
activities = new_client.mechanism.filter(target_chembl_id=node)
compound_ids = [x['molecule_chembl_id'] for x in activities]
approved_drugs = new_client.molecule.filter(molecule_chembl_id__in=compound_ids).filter(max_phase=4)
for drug in approved_drugs:
for key, value in drug.items():
if key=='molecule_chembl_id':
print(value)
However, from this code I only get a very little subset of the results that the paper represented. Could anyone give any suggestions how to get a better search strategy?
Best wishes,
The text was updated successfully, but these errors were encountered: