Batch get protein .pdb files based on Uniprot ID/PDB ID

1. Obtain the protein .pdb file according to the Uniprot ID batch process

Since Uniprot's ID number may correspond to multiple NCBI IDs, but its unique PDB file can be obtained according to Alphafold, so the .pdb file is obtained by code batch processing as follows:

import pandas as pdimport numpy as npfrom Bio import SeqIOfrom Bio import PDBimport requests# But there may be an InsecureRequestWarning warning,# Although it does not affect code collection, but it looks uncomfortable, you can add the following two lines:import urllib3urllib3.disable_warnings()headers = {'User-Agent': 'Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:95.0) Gecko/20100101 Firefox/95.0'}def read_file(file_name):pro_swissProt = []with open(file_name, 'r') as fp:for line in fp:if line.startswith('>'):#Function: Determine whether the string starts with the specified character or substringpro_swissProt.append(line[1:-1])return pro_swissProtfile1 = '/AD/all1.csv'ID=read_file(file1)j = 0not_exist_list = []for i in ID:j = j + 1print(j)print(i)url = 'https://alphafold.ebi.ac.uk/files/AF-'+i+'-F1-model_v1'+'.pdb'print(url)r = requests.get(url, headers=headers, verify=False)with open('/AD/Information/PDB/'+i+'.pdb','w') as files:r = r.text.splitlines() #np.array(pssm).tolist()for lines in r:files.write(lines)files.write('\n')if r[0][1]=='?':print(i + 'No pdb file.')not_exist_list.append(i)#Output the .pdb file of the protein not found, these can be checked manually in the URL, there are omissionsprint(not_exist_list)print(len(not_exist_list))

The format of file1 is as follows:

>Q8BH75MGYDVTRFQGDVDEDLICPICSGVLEEPVQAPHCEHAFCNACITQWFSQQQTCPVDRSVVTVAHLRPVPRIMRNMLSKLQIACDNAVFGCSAVVRLDNLMSHLSDCEHNPKRPVTCEQGCGLEMPKDELPNHNCIKHLRSVVQQQQSRIAELEKTSAEHKHQLAEQKRDIQLLKAYMRAIRSVNPNLQNLEETIEYNEILEWVNSLQPARVTRWGGMISTPDAVLQAVIKRSLVESGCPASIVNELIENAHERSWPQGLATLETRQMNRRYYENYVAKRIPGKQAVVVMACENQHMGDDMVQEPGLVMIFAHGVEEI>P06727MFLKAVVLTLALVAVAGARAEVSADQVATVMWDYFSQLSNNAKEAVEHLQKSELTQQLNALFQDKLGEVNTYAGDLQKKLVPFATELHERLAKDSEKLKEEIGKELEELRARLLPHANEVSQKIGDNLRELQQRLEPYADQLRTQVSTQAEQLRRQLTPYAQRMERVLRENADSLQASLRPHADELKAKIDQNVEELKGRLTPYADEFKVKIDQTVEELRRSLAPYAQDTQEKLNHQLEGLTFQMKKNAEELKARISASAEELRQRLAPLAEDVRGNLRGNTEGLQKSLAELGGHLDQQVEEFRRRVEPYGENFNKALVQQMEQLRQKLGPHAGDVEGHLSFLEKDLRDKVNSFFSTFKEKESQDKTLSLPELEQQQEQQQEQQQEQVQMLAPLES>Q60770MAPPVSERGLKSVVWRKIKTAVFDDCRKEGEWKIMLLDEFTTKLLSSCCKMTDLLEEGITVIENIYKNREPVRQMKALYFISPTPKSVDCFLRDFGSKSEKKYKAAYIYFTDFCPDSLFNKIKASCSKSIRRCKEINISFIPQESQVYTLDVPDAFYYCYSPDPSNASRKEVVMEAMAEQIVTVCATLDENPGVRYKSKPLDNASKLAQLVEKKLEDYYKIDEKGLIKGKTQSQLLIIDRGFDPVSTVLHELTFQAMAYDLLPIENDTYKYKTDGKEKEAVLEEDDDLWVRVRHRHIAVVLEEIPKLMKEISSTKKATEGKTSLSALTQLMKKMPHFRKQISKQVVHLNLAEDCMNKFKLNIEKLCKTEQDLALGTDAEGQRVKDSMLVLLPVLLNKNHDNCDKIRAVLLYIFGINGTTEENLDRLIHNVKIEDDSDMIRNWSHLGVPIVPPSQQAKPLRKDRSAEETFQLSRWTPFIKDIMEDAIDNRLDSKEWPYCSRCPAVWNGSGAVSARQKPRTNYLELDRKNGSRLIIFVIGGITYSEMRCAYEVSQAHKSCEVIIGSTHILTPRKLLDDIKMLNKSKDKVSFKDE>P70452MRDRTHELRQGDNISDDEDEVRVALVVHSGAARLGSPDDEFFQKVQTIRQTMAKLESKVRELEKQQVTILATPLPEESMKQGLQNLREEIKQLGREVRAQLKAIEPQKEEADENYNSVNTRMKKTQHGVLSQQFVELINKCNSMQSEYREKNVERIRRQLKITNAGMVSDEELEQMLDSGQSEVFVSNILKDTQVTRQALNEISARHSEIQQLERSIRELHEIFTFLATEVEMQGEMINRIEKNILSSADYVERGQEHVKIALENQKKARKKKVMIAICVSVTVLILAVIIGITITVG>P63044MSATAATVPPAAPAGEGGPPAPPPNLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYWWKNLKMMIILGVICAIILIIIIVYFST

2. Obtain the pdb file in RCSB according to the PDB ID

Replace the URL of the first piece of code with:

url = 'http://www.rcsb.org/pdb/files/'+i+'.pdb'

PS: I have been learning about dssp processing recently, but there has been no progress, and no friends have Linux installation packages and tutorials

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Full of dry goods said that the quality of my article is too low......, let me submit it and see if the number of words is enough