5
$\begingroup$

Is there any protein database online where I could obtain a list of proteins ordered by the length of their chains / number of amino acids, starting from the shortest, as well as to see their amino acid sequences?

I'd like to start from the short & simple protein structures to see how their particular sequences of amino acids translate into their folding shape, and what those short chains are capable of doing in organisms. (I heard about the LILs, but they are artificially-generated and consist of just two amino acids, Lysine and Isoleucine, so not much variety to study in there :q )

But I'm quite new to these databases, they present a lot of details, but usually not the one I'm looking for, and one has to know what too look for first to get any meaningful information :q

$\endgroup$
  • 1
    $\begingroup$ I like this web quite good :) $\endgroup$ – L.Diago Aug 24 '18 at 1:02
  • $\begingroup$ @aaaaaa: as I said, I'm quite new to those databases, I'm still trying to figure out how to use them. I know some of them, but they don't seem to have any way to list proteins by chain length, starting from the shortest. $\endgroup$ – SasQ Aug 24 '18 at 1:16
  • $\begingroup$ @L.Diago: Yup, this one seems nice, especially the pictures ;) And I see there's an option to search by sequence length. Unfortunately, I can only set the minimum and maximum length, but I don't see any way to order the search results by chain length. There's a "residue count", but I'm not sure if it's the same, since I get some weird resuls :q $\endgroup$ – SasQ Aug 24 '18 at 1:19
  • 2
    $\begingroup$ Have you reviewed the extensive literature on prediction of protein structure? You wouldn't be trying to reinvent the wheel, by any chance? $\endgroup$ – David Aug 24 '18 at 19:05
4
$\begingroup$

You can find the data you need in the Protein Data Bank.

Since 1971, the Protein Data Bank archive (PDB) has served as the single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.

The Worldwide PDB (wwPDB) organization manages the PDB archive and ensures that the PDB is freely and publicly available to the global community.

Each of the PDB member organisations provides the same data with a different interface:

In general, you either query the database through one of the web interfaces, or you download all the data and search it locally. In this case, the RCSB website has the option you asked about (sorting by the residue count):

RCSB search screenshot

Alternatively, you could download: ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt and parse it and sort it as you wish. This file has sequences of all chains in the PDB entries.

But since your goal is to find the relationship between the sequence and the folded structure, you should probably start from reading about the protein folding problem and about methods used in protein structure prediction.

$\endgroup$
  • 3
    $\begingroup$ @SasQ Can you please tune down a bit? You have now three comments flagged and deleted for rudeness, which is not something well liked here. All others: If you want to discuss excessively, please move over to the chat and do not do this in the comments. Thank you. $\endgroup$ – Chris Aug 25 '18 at 9:08
  • $\begingroup$ Comments are not for extended discussion; this conversation has been moved to chat. $\endgroup$ – AliceD Aug 25 '18 at 11:25
  • $\begingroup$ It's worth pointing out that many proteins, and especially "short" ones, are going to be human, computational, or experimental error, or will be intentionally trimmed down from the native version to make it easier to crystallize or otherwise handle. That may not be a problem if considering folding, but relying too much on annotations and descriptions may well be misleading. $\endgroup$ – iayork Oct 12 '18 at 17:08
2
$\begingroup$

In the UniProt Knowledgebase, you can have your proteins sorted by protein length, e.g. in this query for all human proteins with a cross-reference to PDB:

https://www.uniprot.org/uniprot/?query=database%3A(type%3Apdb)%20AND%20organism%3A%22Homo%20sapiens%20(Human)%20%5B9606%5D%22&columns=id%2Centry%20name%2Creviewed%2Cprotein%20names%2Cgenes%2Clength&sort=length

Default sorting is by query score, but if you click on the black triangles in the table headings, e.g. for sequence length, you can have them sorted by other criteria.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.