text: user2034: I'd like to create a dataset consisting of all sequences which are either present in the PDB, or whose homolog is present in the PDB. In other words, any sequence in the PDB or any sequence related to it. The similiarity margin is to be very wide, so anything above, for instance, 25% sequence identity is accepted (perhaps there are better criteria, but you get the point). 
  No further limitations, so any organism, with or without experimental data, not limited to the manually curated Swissprot set. 
  I have tried the SIFTS database, but that contains, as far as I can tell, only mappings for sequence identity >85%. I would like to go far below that. 
  
  user388: You can download a BLAST db containing all sequences of proteins in Uniprot and in the PDB. The way I would go about this is first download the databases for uniprot and PDB, then query the PDB database for each sequence from Uniprot. If you get a BLAST hit above a certain threshold (whatever you define as homolog) then add that sequence to a file, and voila, you have a full set of sequences that fulfill your criteria. The only tools you would need for this are the BLAST executables (found here) and the databases (info on how to download can be found here). 
  I should note that you don't really need any Python to get this to work, only some shell scripting. Although you can run these commands through a Python wrapper if you really want to.
  Good luck!
  
  user266: For the correspondence between PDB and Uniprot entries you can use SIFTS -- a semi-automated mapping between PDB and UniProt maintained by PDBe.
  The pipeline that creates the mappings uses BLAST and a few other criteria to decide which UniProt entry should be assigned to each PDB entry. The SIFTS website has all the data in CSV files.
  
original_text: 2034: <p>I'd like to create a dataset consisting of all sequences which are either present in the PDB, or whose homolog is present in the PDB. In other words, any sequence in the PDB or any sequence related to it. The similiarity margin is to be very wide, so anything above, for instance, 25% sequence identity is accepted (perhaps there are better criteria, but you get the point). </p>
  
  <p>No further limitations, so any organism, with or without experimental data, not limited to the manually curated Swissprot set. </p>
  
  <p>I have tried the SIFTS database, but that contains, as far as I can tell, only mappings for sequence identity >85%. I would like to go far below that. </p>
   388: <p>You can download a BLAST db containing all sequences of proteins in Uniprot and in the PDB. The way I would go about this is first download the databases for uniprot and PDB, then query the PDB database for each sequence from Uniprot. If you get a BLAST hit above a certain threshold (whatever you define as homolog) then add that sequence to a file, and voila, you have a full set of sequences that fulfill your criteria. The only tools you would need for this are the BLAST executables (<a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download" rel="nofollow noreferrer">found here</a>) and the databases (info on how to download can be found <a href="https://www.ncbi.nlm.nih.gov/books/NBK62345/#_blast_ftp_site_The_blastdb_subdirectory_" rel="nofollow noreferrer">here</a>). </p>
  
  <p>I should note that you don't really need any Python to get this to work, only some shell scripting. Although you can run these commands through a Python wrapper if you really want to.</p>
  
  <p>Good luck!</p>
   266: <p>For the correspondence between PDB and Uniprot entries you can use <a href="https://www.ebi.ac.uk/pdbe/docs/sifts/" rel="nofollow noreferrer">SIFTS</a> -- a semi-automated mapping between PDB and UniProt maintained by PDBe.</p>
  
  <p>The pipeline that creates the mappings uses BLAST and <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531078/" rel="nofollow noreferrer">a few other criteria</a> to decide which UniProt entry should be assigned to each PDB entry. The SIFTS website has all the data in CSV files.</p>
  