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,
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,