Search on uniprot¶

You can search on uniprot to find uniprot accessions and structure identifiers.

In [23]:

# Setup some logging
import logging
from pprint import pprint

logging.basicConfig(level=logging.WARNING)
# Set to WARNING to see only warnings
# Set to INFO to see sparql queries
# Set to DEBUG to see raw results

# Setup some logging import logging from pprint import pprint logging.basicConfig(level=logging.WARNING) # Set to WARNING to see only warnings # Set to INFO to see sparql queries # Set to DEBUG to see raw results

Search for uniprot acessions based on a query¶

In [24]:

from protein_quest.uniprot import Query, search4uniprot

from protein_quest.uniprot import Query, search4uniprot

In [25]:

query = Query(
    taxon_id="9606",
    reviewed=True,
    subcellular_location_uniprot="nucleus",
    subcellular_location_go=["GO:0005634"],  # Cellular component - Nucleus
    molecular_function_go=["GO:0003677"],  # Molecular function - DNA binding
)

query = Query( taxon_id="9606", reviewed=True, subcellular_location_uniprot="nucleus", subcellular_location_go=["GO:0005634"], # Cellular component - Nucleus molecular_function_go=["GO:0003677"], # Molecular function - DNA binding )

In [26]:

uniprot_accessions = search4uniprot(query, limit=200)

uniprot_accessions = search4uniprot(query, limit=200)

WARNING:protein_quest.uniprot:Search for uniprot accessions returned 200 results. There may be more results available, but they are not returned due to the limit of 200. Consider increasing the limit to get more results.

In [27]:

print(f"Number of Uniprot accessions: {len(uniprot_accessions)}")
print("First 5:")
pprint(list(uniprot_accessions)[:5])
print("Last 5:")
pprint(list(uniprot_accessions)[-5:])

print(f"Number of Uniprot accessions: {len(uniprot_accessions)}") print("First 5:") pprint(list(uniprot_accessions)[:5]) print("Last 5:") pprint(list(uniprot_accessions)[-5:])

Number of Uniprot accessions: 200
First 5:
['O43435', 'O43364', 'O14627', 'O43151', 'O43913']
Last 5:
['O15266', 'O60393', 'A8K8V0', 'A8MUV8', 'O14746']

Find Protein Data Bank (PDB) entries for uniprot entries¶

In [28]:

from protein_quest.uniprot import search4pdb

from protein_quest.uniprot import search4pdb

In [29]:

pdb_results = search4pdb(uniprot_accessions, limit=200)

pdb_results = search4pdb(uniprot_accessions, limit=200)

WARNING:protein_quest.uniprot:Search for pdbs on uniprot returned 200 results. There may be more results available, but they are not returned due to the limit of 200. Consider increasing the limit to get more results.

In [30]:

pprint(f"Number of PDB results: {len(pdb_results)}")
pprint("First 5 PDBs of first Uniprot entry:")
first_uniprot = next(iter(pdb_results.items()))
pprint(first_uniprot[0])
pprint(list(first_uniprot[1])[:5])

pprint(f"Number of PDB results: {len(pdb_results)}") pprint("First 5 PDBs of first Uniprot entry:") first_uniprot = next(iter(pdb_results.items())) pprint(first_uniprot[0]) pprint(list(first_uniprot[1])[:5])

'Number of PDB results: 46'
'First 5 PDBs of first Uniprot entry:'
'O15350'
[PdbResult(id='2WQI',
           method='X-Ray_Crystallography',
           uniprot_chains='A/B/C/D=351-399',
           resolution='1.7'),
 PdbResult(id='4G83',
           method='X-Ray_Crystallography',
           uniprot_chains='A/B=115-312',
           resolution='4'),
 PdbResult(id='2XWC',
           method='X-Ray_Crystallography',
           uniprot_chains='A=112-311',
           resolution='1.82'),
 PdbResult(id='2KBY',
           method='NMR_Spectroscopy',
           uniprot_chains='A/B/C/D=351-398',
           resolution=None),
 PdbResult(id='2WQJ',
           method='X-Ray_Crystallography',
           uniprot_chains='1/2/A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X/Y/Z=351-383',
           resolution='2')]

Find AlphaFold models for uniprot entries¶

In [31]:

from protein_quest.uniprot import search4af

from protein_quest.uniprot import search4af

In [32]:

afresults = search4af(uniprot_accessions, limit=200)

afresults = search4af(uniprot_accessions, limit=200)

In [33]:

pprint(f"Number of AlphaFold results: {len(afresults)}")
first_af = next(iter(afresults.items()))
pprint(first_af)

pprint(f"Number of AlphaFold results: {len(afresults)}") first_af = next(iter(afresults.items())) pprint(first_af)

'Number of AlphaFold results: 198'
('A0A087WUV0', {'A0A087WUV0'})

Find Electron Microscopy Data Bank (EMDB) entries for uniprot entries¶

In [34]:

from protein_quest.uniprot import search4emdb

from protein_quest.uniprot import search4emdb

In [35]:

uniprot_accessions = search4emdb(uniprot_accessions, limit=200)

uniprot_accessions = search4emdb(uniprot_accessions, limit=200)

In [36]:

pprint(f"Number of Uniprot accessions with EMDB entries: {len(uniprot_accessions)}")
first_uniprot = next(iter(uniprot_accessions.items()))
pprint(first_uniprot)

pprint(f"Number of Uniprot accessions with EMDB entries: {len(uniprot_accessions)}") first_uniprot = next(iter(uniprot_accessions.items())) pprint(first_uniprot)

'Number of Uniprot accessions with EMDB entries: 22'
('O14497', {'EMD-0974'})