#Подключаем необходимые модули
!pip install nglview --user
import nglview as nv
import requests # Этот стандартный модуль позволяет посылать запросы к веб-ресурсам
import json
#Формируем запрос
my_query = {
"query": {
"type": "group",
"logical_operator": "and",
"nodes": [
{
#name
"type": "terminal",
"service": "text",
"parameters": {
"value": "ampicillin",
"attribute": "struct.title",
"operator": "contains_words"}
},
{
#resolution
"type": "terminal",
"service": "text",
"parameters": {
"value": 2.5,
"operator": "less_or_equal",
"attribute": "rcsb_entry_info.resolution_combined"
}
},
{
#ligands
"type": "terminal",
"service": "text",
"parameters": {
"attribute": "rcsb_entry_info.nonpolymer_entity_count",
"value": 0,
"operator": "greater"
}
},
{
#date
"type": "terminal",
"service": "text",
"parameters": {
"attribute": "rcsb_accession_info.initial_release_date",
"value": {
"from": "2010-01-01",
"to": "2015-01-01"
},
"operator": "range"
}
}
]
},
"return_type": "entry"
}
#2. Отправляем запрос
rcsb = 'https://search.rcsb.org/rcsbsearch/v1/query'
json_query = json.dumps(my_query)
search = requests.post(f'{rcsb}', data=json_query)
search_result = search.json()
search_result
/usr/lib/python3/dist-packages/secretstorage/dhcrypto.py:15: CryptographyDeprecationWarning: int_from_bytes is deprecated, use int.from_bytes instead
from cryptography.utils import int_from_bytes
/usr/lib/python3/dist-packages/secretstorage/util.py:19: CryptographyDeprecationWarning: int_from_bytes is deprecated, use int.from_bytes instead
from cryptography.utils import int_from_bytes
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WARNING: You are using pip version 21.0.1; however, version 22.0.3 is available.
You should consider upgrading via the '/usr/bin/python3 -m pip install --upgrade pip' command.
{'query_id': 'ac3a7223-8bdc-4ab5-b017-8cda31f4caef',
'result_type': 'entry',
'total_count': 9,
'result_set': [{'identifier': '3N8L',
'score': 1.0,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 14068,
'original_score': 194.04849243164062,
'norm_score': 1.0}]}]},
{'identifier': '4GCP',
'score': 0.619623732298679,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 14068,
'original_score': 180.5673065185547,
'norm_score': 0.619623732298679}]}]},
{'identifier': '2WKH',
'score': 0.2893915205871767,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 14068,
'original_score': 168.86331176757812,
'norm_score': 0.2893915205871767}]}]},
{'identifier': '3NDV',
'score': 0.2893915205871767,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 14068,
'original_score': 168.86331176757812,
'norm_score': 0.2893915205871767}]}]},
{'identifier': '4HL2',
'score': 0.2893915205871767,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 14068,
'original_score': 168.86331176757812,
'norm_score': 0.2893915205871767}]}]},
{'identifier': '3NFB',
'score': 0.14007916621460811,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 14068,
'original_score': 163.57142639160156,
'norm_score': 0.14007916621460811}]}]},
{'identifier': '4HL1',
'score': 0.14007916621460811,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 14068,
'original_score': 163.57142639160156,
'norm_score': 0.14007916621460811}]}]},
{'identifier': '3ZG8',
'score': 0.0,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 14068,
'original_score': 158.60678100585938,
'norm_score': 0.0}]}]},
{'identifier': '4RAW',
'score': 0.0,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 14068,
'original_score': 158.60678100585938,
'norm_score': 0.0}]}]}]}
best_hit = search_result["result_set"][0]
best_hit
{'identifier': '3N8L',
'score': 1.0,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 14068,
'original_score': 194.04849243164062,
'norm_score': 1.0}]}]}
4GCP является структурой порина E.coli, связанного с антибиотиком ампициллином (чьё название было ключевым словом в запросе).
Структура показывает, что ток через порин блокируется связанным ампициллином
view = nv.show_pdbid('4GCP')
view
Белок в виде cartoon, покраска по типу вторичной структуры
Показана поверхность, с непрозрачностью 0.1
Лиганды в виде hyperball, покрашены в оттенок желтого на ваш выбор
#var3
view = nv.show_pdbid("4GCP", default_representation=False)
view.add_representation("cartoon", selection="protein", color="sstruc")
view.add_representation('surface', selection='protein', color='purple', opacity=0.1)
view.add_representation('hyperball', selection='ligand', color='yellow')
view.center()
view
Поверхность белка покрашена в белый, с непрозрачностью 0.1
Белок в виде cartoon темно-серого цвета
Боковые радикалы в стержневой модели, покрашены по гидрофобности
Лиганды в виде Ван-дер-Ваальсовых сфер, покрашены по элементам
#var8
view = nv.show_pdbid("4GCP", default_representation=False)
view.add_representation("cartoon", selection="protein", color="dark gray")
view.add_representation('surface', selection='protein', color='white', opacity=0.1)
view.add_representation('element', selection='ligand', color='spacefill')
view.add_representation('licorice', selection='sidechainAttached', color='hydrophobicity')
view.center()
view
Остов белка в шаростержневой модели, покрашен по элементам
Боковые радикалы в стержневой модели, покрашены по элементам
Углероды остатков с 30 по 70-й покрашены в светло-голубой < Лиганды показаны в виде линий, покрашены в любой оттенок оранжевого#var9
view = nv.show_pdbid("4GCP", default_representation=False)
view.add_representation("ball+stick", selection="backbone", color="element")
view.add_representation('licorice', selection='sidechain', color='element', opacity=0.1)
view.add_representation('ball+stick', selection='protein and :A and 30-70 and _C', color='lightblue')
view.add_representation('line', selection='ligand', color='orange')
view.center()
view