AlphaFold¶
You can download and filter AlphaFold files on confidence.
Environment setup¶
Run the next cell once per fresh kernel to install notebook dependencies. If you install packages in the active kernel, restart the kernel and rerun all cells.
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# Cloud and local notebooks: install required runtime dependencies.
%pip install -q protein-quest[nb]
# Cloud and local notebooks: install required runtime dependencies.
%pip install -q protein-quest[nb]
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# Generic imports
import logging
from pathlib import Path
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
# Generic imports
import logging
from pathlib import Path
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
Download Alphafold files¶
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from protein_quest.alphafold.fetch import fetch_many_async
from protein_quest.alphafold.fetch import fetch_many_async
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save_dir = Path("alphafold_files")
save_dir = Path("alphafold_files")
To download the summary, the cif and predicted Aligned error document (peaDoc) file for 3 AlphaFold entries given their uniprot accessions.
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summaries = [ # pyrefly: ignore[invalid-syntax]
s async for s in fetch_many_async(["A1YPR0", "O60481", "P50613"], save_dir, formats={"summary", "cif", "paeDoc"})
]
pprint(summaries)
summaries = [ # pyrefly: ignore[invalid-syntax]
s async for s in fetch_many_async(["A1YPR0", "O60481", "P50613"], save_dir, formats={"summary", "cif", "paeDoc"})
]
pprint(summaries)
Fetching Alphafold summaries: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 3/3 [00:00<00:00, 20.74it/s] Downloading AlphaFold files: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 6/6 [00:00<00:00, 19.60it/s]
[AlphaFoldEntry(uniprot_accession='A1YPR0',
summary=EntrySummary(allVersions=[1, 2, 3, 4, 5, 6],
bcifUrl=URL('https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-model_v6.bcif'),
cifUrl=URL('https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-model_v6.cif'),
entityType='protein',
fractionPlddtConfident=0.26,
fractionPlddtLow=0.099,
fractionPlddtVeryHigh=0.089,
fractionPlddtVeryLow=0.553,
globalMetricValue=56.03,
isUniProt=True,
latestVersion=6,
modelCreatedDate='2025-08-01T00:00:00Z',
modelEntityId='AF-A1YPR0-F1',
paeDocUrl=URL('https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-predicted_aligned_error_v6.json'),
pdbUrl=URL('https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-model_v6.pdb'),
providerId='GDM',
sequence='MANDIDELIGIPFPNHSSEVLCSLNEQRHDGLLCDVLLVVQEQEYRTHRSVLAACSKYFKKLFTAGTLASQPYVYEIDFVQPEALAAILEFAYTSTLTITAGNVKHILNAARMLEIQCIVNVCLEIMEPGGDGGEEDDKEDDDDDEDDDDEEDEEEEEEEEEDDDDDTEDFADQENLPDPQDISCHQSPSKTDHLTEKAYSDTPRDFPDSFQAGSPGHLGVIRDFSIESLLRENLYPKANIPDRRPSLSPFAPDFFPHLWPGDFGAFAQLPEQPMDSGPLDLVIKNRKIKEEEKEELPPPPPPPFPNDFFKDMFPDLPGGPLGPIKAENDYGAYLNFLSATHLGGLFPPWPLVEERKLKPKASQQCPICHKVIMGAGKLPRHMRTHTGEKPYMCTICEVRFTRQDKLKIHMRKHTGERPYLCIHCNAKFVHNYDLKNHMRIHTGVRPYQCEFCYKSFTRSDHLHRHIKRQSCRMARPRRGRKPAAWRAASLLFGPGGPAPDKAAFVMPPALGEVGGHLGGAAVCLPGPSPAKHFLAAPKGALSLQELERQFEETQMKLFGRAQLEAERNAGGLLAFALAENVAAARPYFPLPDPWAAGLAGLPGLAGLNHVASMSEANN',
sequenceChecksum='455da6445b69ec9853216a00638d635b',
sequenceEnd=619,
sequenceStart=1,
sequenceVersionDate='2007-02-06T00:00:00Z',
toolUsed='AlphaFold Monomer v2.0 pipeline',
alternativeNames=None,
amAnnotationsHg19Url=URL('https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-hg19.csv'),
amAnnotationsHg38Url=URL('https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-hg38.csv'),
amAnnotationsUrl=URL('https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-aa-substitutions.csv'),
catalyticActivities=None,
complexName=None,
functions=None,
gene='ZBTB7C',
geneSynonyms=None,
ipSAE=None,
ipTM=None,
isUniProtReferenceProteome=True,
isUniProtReviewed=True,
keywords=None,
msaUrl=URL('https://alphafold.ebi.ac.uk/files/msa/AF-A1YPR0-F1-msa_v6.a3m'),
organismCommonNames=None,
organismScientificName='Homo sapiens',
organismSynonyms=None,
plddtDocUrl=URL('https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-confidence_v6.json'),
proteinFullNames=None,
proteinShortNames=None,
stoichiometry=None,
taxId=9606,
taxonomyLineage=None,
uniprotAccession='A1YPR0',
uniprotDescription='Zinc finger and BTB '
'domain-containing '
'protein 7C',
uniprotId='ZBT7C_HUMAN'),
summary_file=PosixPath('alphafold_files/A1YPR0.json'),
bcif_file=None,
cif_file=PosixPath('alphafold_files/AF-A1YPR0-F1-model_v6.cif'),
pdb_file=None,
pae_doc_file=PosixPath('alphafold_files/AF-A1YPR0-F1-predicted_aligned_error_v6.json'),
am_annotations_file=None,
am_annotations_hg19_file=None,
am_annotations_hg38_file=None,
msa_file=None,
plddt_doc_file=None),
AlphaFoldEntry(uniprot_accession='O60481',
summary=EntrySummary(allVersions=[1, 2, 3, 4, 5, 6],
bcifUrl=URL('https://alphafold.ebi.ac.uk/files/AF-O60481-F1-model_v6.bcif'),
cifUrl=URL('https://alphafold.ebi.ac.uk/files/AF-O60481-F1-model_v6.cif'),
entityType='protein',
fractionPlddtConfident=0.289,
fractionPlddtLow=0.107,
fractionPlddtVeryHigh=0.0,
fractionPlddtVeryLow=0.604,
globalMetricValue=53.88,
isUniProt=True,
latestVersion=6,
modelCreatedDate='2025-08-01T00:00:00Z',
modelEntityId='AF-O60481-F1',
paeDocUrl=URL('https://alphafold.ebi.ac.uk/files/AF-O60481-F1-predicted_aligned_error_v6.json'),
pdbUrl=URL('https://alphafold.ebi.ac.uk/files/AF-O60481-F1-model_v6.pdb'),
providerId='GDM',
sequence='MTMLLDGGPQFPGLGVGSFGAPRHHEMPNREPAGMGLNPFGDSTHAAAAAAAAAAFKLSPAAAHDLSSGQSSAFTPQGSGYANALGHHHHHHHHHHHTSQVPSYGGAASAAFNSTREFLFRQRSSGLSEAASGGGQHGLFAGSASSLHAPAGIPEPPSYLLFPGLHEQGAGHPSPTGHVDNNQVHLGLRGELFGRADPYRPVASPRTDPYAAGAQFPNYSPMNMNMGVNVAAHHGPGAFFRYMRQPIKQELSCKWIDEAQLSRPKKSCDRTFSTMHELVTHVTMEHVGGPEQNNHVCYWEECPREGKSFKAKYKLVNHIRVHTGEKPFPCPFPGCGKIFARSENLKIHKRTHTGEKPFKCEFEGCDRRFANSSDRKKHMHVHTSDKPYICKVCDKSYTHPSSLRKHMKVHESQGSDSSPAASSGYESSTPPAIASANSKDTTKTPSAVQTSTSHNPGLPPNFNEWYV',
sequenceChecksum='b2daa0c0f3120f23c7fe601510d1082e',
sequenceEnd=467,
sequenceStart=1,
sequenceVersionDate='1998-08-01T00:00:00Z',
toolUsed='AlphaFold Monomer v2.0 pipeline',
alternativeNames=None,
amAnnotationsHg19Url=URL('https://alphafold.ebi.ac.uk/files/AF-O60481-F1-hg19.csv'),
amAnnotationsHg38Url=URL('https://alphafold.ebi.ac.uk/files/AF-O60481-F1-hg38.csv'),
amAnnotationsUrl=URL('https://alphafold.ebi.ac.uk/files/AF-O60481-F1-aa-substitutions.csv'),
catalyticActivities=None,
complexName=None,
functions=None,
gene='ZIC3',
geneSynonyms=None,
ipSAE=None,
ipTM=None,
isUniProtReferenceProteome=True,
isUniProtReviewed=True,
keywords=None,
msaUrl=URL('https://alphafold.ebi.ac.uk/files/msa/AF-O60481-F1-msa_v6.a3m'),
organismCommonNames=None,
organismScientificName='Homo sapiens',
organismSynonyms=None,
plddtDocUrl=URL('https://alphafold.ebi.ac.uk/files/AF-O60481-F1-confidence_v6.json'),
proteinFullNames=None,
proteinShortNames=None,
stoichiometry=None,
taxId=9606,
taxonomyLineage=None,
uniprotAccession='O60481',
uniprotDescription='Zinc finger protein '
'ZIC 3',
uniprotId='ZIC3_HUMAN'),
summary_file=PosixPath('alphafold_files/O60481.json'),
bcif_file=None,
cif_file=PosixPath('alphafold_files/AF-O60481-F1-model_v6.cif'),
pdb_file=None,
pae_doc_file=PosixPath('alphafold_files/AF-O60481-F1-predicted_aligned_error_v6.json'),
am_annotations_file=None,
am_annotations_hg19_file=None,
am_annotations_hg38_file=None,
msa_file=None,
plddt_doc_file=None),
AlphaFoldEntry(uniprot_accession='P50613',
summary=EntrySummary(allVersions=[1, 2, 3, 4, 5, 6],
bcifUrl=URL('https://alphafold.ebi.ac.uk/files/AF-P50613-F1-model_v6.bcif'),
cifUrl=URL('https://alphafold.ebi.ac.uk/files/AF-P50613-F1-model_v6.cif'),
entityType='protein',
fractionPlddtConfident=0.127,
fractionPlddtLow=0.092,
fractionPlddtVeryHigh=0.618,
fractionPlddtVeryLow=0.162,
globalMetricValue=82.0,
isUniProt=True,
latestVersion=6,
modelCreatedDate='2025-08-01T00:00:00Z',
modelEntityId='AF-P50613-F1',
paeDocUrl=URL('https://alphafold.ebi.ac.uk/files/AF-P50613-F1-predicted_aligned_error_v6.json'),
pdbUrl=URL('https://alphafold.ebi.ac.uk/files/AF-P50613-F1-model_v6.pdb'),
providerId='GDM',
sequence='MALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQWPDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSNRPGPTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEALEQGGLPKKLIF',
sequenceChecksum='efac0ba2abc8f0b14c6b6689a0f2d676',
sequenceEnd=346,
sequenceStart=1,
sequenceVersionDate='1996-10-01T00:00:00Z',
toolUsed='AlphaFold Monomer v2.0 pipeline',
alternativeNames=None,
amAnnotationsHg19Url=URL('https://alphafold.ebi.ac.uk/files/AF-P50613-F1-hg19.csv'),
amAnnotationsHg38Url=URL('https://alphafold.ebi.ac.uk/files/AF-P50613-F1-hg38.csv'),
amAnnotationsUrl=URL('https://alphafold.ebi.ac.uk/files/AF-P50613-F1-aa-substitutions.csv'),
catalyticActivities=None,
complexName=None,
functions=None,
gene='CDK7',
geneSynonyms=None,
ipSAE=None,
ipTM=None,
isUniProtReferenceProteome=True,
isUniProtReviewed=True,
keywords=None,
msaUrl=URL('https://alphafold.ebi.ac.uk/files/msa/AF-P50613-F1-msa_v6.a3m'),
organismCommonNames=None,
organismScientificName='Homo sapiens',
organismSynonyms=None,
plddtDocUrl=URL('https://alphafold.ebi.ac.uk/files/AF-P50613-F1-confidence_v6.json'),
proteinFullNames=None,
proteinShortNames=None,
stoichiometry=None,
taxId=9606,
taxonomyLineage=None,
uniprotAccession='P50613',
uniprotDescription='Cyclin-dependent '
'kinase 7',
uniprotId='CDK7_HUMAN'),
summary_file=PosixPath('alphafold_files/P50613.json'),
bcif_file=None,
cif_file=PosixPath('alphafold_files/AF-P50613-F1-model_v6.cif'),
pdb_file=None,
pae_doc_file=PosixPath('alphafold_files/AF-P50613-F1-predicted_aligned_error_v6.json'),
am_annotations_file=None,
am_annotations_hg19_file=None,
am_annotations_hg38_file=None,
msa_file=None,
plddt_doc_file=None)]
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!ls -sh {save_dir}
!ls -sh {save_dir}
total 3.3M 4.0K A1YPR0.json 556K AF-A1YPR0-F1-model_v6.cif 1.1M AF-A1YPR0-F1-predicted_aligned_error_v6.json 412K AF-O60481-F1-model_v6.cif 628K AF-O60481-F1-predicted_aligned_error_v6.json 324K AF-P50613-F1-model_v6.cif 276K AF-P50613-F1-predicted_aligned_error_v6.json 8.0K O60481.json 4.0K P50613.json
Filter AlphFold structure files on confidence¶
Filter AlphaFold mmcif/PDB files by confidence (plDDT). Passed files are written with residues below threshold removed.
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from protein_quest.alphafold.confidence import ConfidenceFilterQuery, filter_files_on_confidence
from protein_quest.alphafold.confidence import ConfidenceFilterQuery, filter_files_on_confidence
Take one of the downloaded files
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input_files = [entry.cif_file for entry in summaries if entry.cif_file is not None]
input_files
input_files = [entry.cif_file for entry in summaries if entry.cif_file is not None]
input_files
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[PosixPath('alphafold_files/AF-A1YPR0-F1-model_v6.cif'),
PosixPath('alphafold_files/AF-O60481-F1-model_v6.cif'),
PosixPath('alphafold_files/AF-P50613-F1-model_v6.cif')]
We only write a filtered cif file when in the input file there are between 100 and 1000 residues that have a pLDDT score above 50.
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query = ConfidenceFilterQuery(confidence=80, min_residues=100, max_residues=1000)
query = ConfidenceFilterQuery(confidence=80, min_residues=100, max_residues=1000)
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output_dir = Path("./filtered")
output_dir.mkdir(exist_ok=True)
result = filter_files_on_confidence(input_files, query, output_dir)
output_dir = Path("./filtered")
output_dir.mkdir(exist_ok=True)
result = filter_files_on_confidence(input_files, query, output_dir)
[########################################] | 100% Completed | 0.1s
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list(
filter_files_on_confidence(
input_files, ConfidenceFilterQuery(confidence=80, min_residues=100, max_residues=1000), output_dir
)
)
list(
filter_files_on_confidence(
input_files, ConfidenceFilterQuery(confidence=80, min_residues=100, max_residues=1000), output_dir
)
)
WARNING:protein_quest.parallel:Not using all CPU cores (6) of machine, environment variable "OMP_NUM_THREADS" is set to 1. [########################################] | 100% Completed | 0.1s
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[ConfidenceFilterResult(input_file='AF-A1YPR0-F1-model_v6.cif', count=199, filtered_file=PosixPath('filtered/AF-A1YPR0-F1-model_v6.cif')),
ConfidenceFilterResult(input_file='AF-O60481-F1-model_v6.cif', count=67, filtered_file=None),
ConfidenceFilterResult(input_file='AF-P50613-F1-model_v6.cif', count=248, filtered_file=PosixPath('filtered/AF-P50613-F1-model_v6.cif'))]
2 files have passed, but 1 file only has 75 high confidence residues so it is discarded.
Visualize structures with Mol*¶
Use molviewspec to visualize the structures.
Cell output is absent to keep notebook size small, please run yourself to see visualization.
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from molviewspec import ContinuousPalette, GlobalMetadata, States, create_builder, molstar_notebook
snapshots = []
# Structure data is embedded into visualization to keep it portable
data = {}
for summary in summaries:
structure_file = summary.cif_file
if not structure_file:
continue
builder = create_builder()
structure = builder.download(url=structure_file.name).parse(format="mmcif").model_structure()
structure.component(selector="polymer").representation().color_from_source(
schema="all_atomic",
category_name="atom_site",
field_name="B_iso_or_equiv",
palette=ContinuousPalette(colors="RdYlBu"),
)
structure.component().tooltip(text="pLDDT:")
structure.tooltip_from_source(schema="all_atomic", category_name="atom_site", field_name="B_iso_or_equiv")
data[structure_file.name] = structure_file.read_bytes()
snapshot = builder.get_snapshot(title=structure_file.name)
snapshots.append(snapshot)
molstar_notebook(
state=States(snapshots=snapshots, metadata=GlobalMetadata(description="Alphafold structures")),
data=data,
width="100%",
height=900,
)
from molviewspec import ContinuousPalette, GlobalMetadata, States, create_builder, molstar_notebook
snapshots = []
# Structure data is embedded into visualization to keep it portable
data = {}
for summary in summaries:
structure_file = summary.cif_file
if not structure_file:
continue
builder = create_builder()
structure = builder.download(url=structure_file.name).parse(format="mmcif").model_structure()
structure.component(selector="polymer").representation().color_from_source(
schema="all_atomic",
category_name="atom_site",
field_name="B_iso_or_equiv",
palette=ContinuousPalette(colors="RdYlBu"),
)
structure.component().tooltip(text="pLDDT:")
structure.tooltip_from_source(schema="all_atomic", category_name="atom_site", field_name="B_iso_or_equiv")
data[structure_file.name] = structure_file.read_bytes()
snapshot = builder.get_snapshot(title=structure_file.name)
snapshots.append(snapshot)
molstar_notebook(
state=States(snapshots=snapshots, metadata=GlobalMetadata(description="Alphafold structures")),
data=data,
width="100%",
height=900,
)
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