Практикум 1. Поиск в PDB и основы визуализации

Установка внешнего пакета nglview:

!pip install nglview --user 

/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 22.0.4 is available.
You should consider upgrading via the '/usr/bin/python3 -m pip install --upgrade pip' command.

Импорт всего необходимого:

import nglview as nv
import requests
import json

Задание 1

С помощью кода ищем наиболее подходящую запись из банка PDB, соответсвующую запросу:

my_query = {
    "query": {
        "type": "group",
        "logical_operator": "and",
        "nodes": []
    },
    "return_type": "entry"
}

Ключевое слово - riboflavin, поиск в заголовке:

keyword_clause = {
    "type": "terminal",
    "service": "text", 
    "parameters": {
        "value": "riboflavin",
        "attribute": "struct.title",
        "operator": "contains_words"
    }
}

my_query["query"]["nodes"].append(keyword_clause)

Разрешение не хуже 2 ангстрем:

resolution_clause = {
    "type": "terminal",
    "service": "text",
    "parameters": {
        "value": 2.0,
        "attribute": "rcsb_entry_info.resolution_combined",
        "operator": "less_or_equal"
    }
}

my_query["query"]["nodes"].append(resolution_clause)

Лигандов не меньше 2:

has_ligand_clause = {
    "type": "terminal",
    "service": "text",
    "parameters": {
        "attribute": "rcsb_entry_info.nonpolymer_entity_count",
        "value": 1,
        "operator": "greater"
    }
}

my_query["query"]["nodes"].append(has_ligand_clause)

Дата публикации записи: с 1 января 2020 по 1 января 2023:

date_range_clause = {
    "type": "terminal",
    "service": "text",
    "parameters": {
        "attribute": "rcsb_accession_info.initial_release_date",
        "value": {
            "from": "2020-01-01", 
            "to": "2023-01-01",
        },
        "operator": "range"
    }
}

my_query["query"]["nodes"].append(date_range_clause)

Отсылаем запрос на сервер RSCB в виде JSON-строки:

rcsb = 'https://search.rcsb.org/rcsbsearch/v1/query'

json_query = json.dumps(my_query)

search = requests.post(f'{rcsb}', data=json_query) 

search

<Response [200]>

Код 200 означает, что все прошло правильно

search_result = search.json() # Распаковываем ответ сервера в словарь
search_result

{'query_id': '8b030ea0-c57c-4204-88e8-2bdf6c00c4ea',
 'result_type': 'entry',
 'total_count': 3,
 'result_set': [{'identifier': '7QF2',
   'score': 1.0,
   'services': [{'service_type': 'text',
     'nodes': [{'node_id': 229,
       'original_score': 181.88107299804688,
       'norm_score': 1.0}]}]},
  {'identifier': '7PD9',
   'score': 0.5611051500181274,
   'services': [{'service_type': 'text',
     'nodes': [{'node_id': 229,
       'original_score': 163.59376525878906,
       'norm_score': 0.5611051500181274}]}]},
  {'identifier': '7QF4',
   'score': 0.0,
   'services': [{'service_type': 'text',
     'nodes': [{'node_id': 229,
       'original_score': 140.21435546875,
       'norm_score': 0.0}]}]}]}

Выбираем лучшую находку:

best_hit = search_result["result_set"][0] 
best_hit

{'identifier': '7QF2',
 'score': 1.0,
 'services': [{'service_type': 'text',
   'nodes': [{'node_id': 229,
     'original_score': 181.88107299804688,
     'norm_score': 1.0}]}]}

Таким образом, я далее буду работать с PDB ID 7QF2

Задание 2

Найденная по идентификатору запись соответствует белку, который участвует в производстве синглетного кислорода, с рибофлавином в качестве кофактора. Авторы данного исследования модифицировали белок miniSOG, пытаясь улучшить его свойства. Им удалось увеличить выход кислорода путем замены флавинмононуклеотида на рибофлавин.

Задание 3

Импорт всего необходимого:

from ipywidgets import interact, fixed

Создание отображений с заданными параметрами:

my_examples = {
    'Example 5': {
        'description': '''
Белок в виде tube, покраска по типу вторичной структуры
Боковые радикалы в стержневой модели, покрашены по гидрофобности
Лиганды показаны линиями, покрашены по элементам
Вода и ионы показаны в виде Ван-дер-Ваальсовых сфер
''',
        'representations': [
            {
                'type': 'tube',                      
                'params': {
                    'sele': 'protein',              
                    'color': 'sstruc'
                 }
            },
            {
                'type': 'licorice',
                'params': {
                    'sele': 'sidechainAttached',                 
                    'color': 'hydrophobicity'  
                 }
            },
            {
                'type': 'line',                      
                'params': {
                    'sele': 'ligand',                
                    'color': 'element'  
                 }
            },
            {
                'type': 'spacefill',                      
                'params': {
                    'sele': 'ion or water'
                 }
            },
        ],
    },
    'Example 7': {
        'description': '''
Белок в виде ribbon, покрашенной градиентом от N к C концу
Боковые радикалы в стержневой модели, покрашенные по элементам
Углероды гидрофобных аминокислот покрашены в светло-желтый
Углероды полярных заряженных аминокислот покрашены в светло-голубой
Лиганды не показаны никак
''',
        'representations': [
            {
                'type': 'ribbon',                      
                'params': {
                    'sele': 'protein',               
                    'color': 'residueindex'  
                 }
            },
            {
                'type': 'licorice',                      
                'params': {
                    'sele': 'sidechainAttached',                     
                    'color': 'element'  
                 }
            },
            {
                'type': 'licorice',                      
                'params': {
                    'sele': 'hydrophobic and _C',                     
                    'color': 'lightyellow'  
                 }
            },
            {
                'type': 'licorice',
                'params': {
                    'sele': 'charged and _C',
                    'color': 'lightblue'
                }
            },
        ],
    },
   'Example 10': {
        'description': '''
Белок в виде cartoon белого цвета
Cartoon для остатков с 20-го по 55-й покрашен в зеленый
Для остатков с 20-го по 55-й показаны боковые радикалы в модели hyperball, покраска по элементам
Лиганды показаны в шаростержневой модели, покраска по элементам
''',
        'representations': [
            {
                'type': 'cartoon',                      
                'params': {
                    'sele': 'protein',               
                    'color': 'white'  
                 }
            },
            {
                'type': 'cartoon',                      
                'params': {
                    'sele': 'protein and 20-55',                     
                    'color': 'green'  
                 }
            },
            {
                'type': 'hyperball',                      
                'params': {
                    'sele': 'sidechainAttached and 20-55',                     
                    'color': 'element'  
                 }
            },
            {
                'type': 'ball+stick',
                'params': {
                    'sele': 'ligand',                     
                    'color': 'element'  
                 }
            },
        ],
    },
}
   

def show_examples(view, example_name):   
    view.clear()
    example = my_examples[example_name]
    print(example['description'])
    view.set_representations(example['representations'])
    view.center()

view = nv.show_pdbid("7qf2", default_representation=False)
interact(show_examples, view=fixed(view), example_name=list(my_examples.keys()))
view