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Is there a way to search to search for specific structural motifs in proteins? For example can a database where we can find structures with zing finger motif or an hairpin...

PDBeMotif (ebi.ac.uk) has some motifs for example but no way to download them. Small Three-Dimensional Protein Motifs (gla.ac.uk) also offers some.

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  • $\begingroup$ Do you have a sequence of amino acids for making the search? $\endgroup$
    – Vasista
    Oct 28, 2021 at 6:18
  • $\begingroup$ yeah for some motif, but not all of them. They are not sequence dependent, just make similar structural fold. $\endgroup$
    – BND
    Oct 28, 2021 at 7:36
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    $\begingroup$ for some motifs then you can use that sequence and run it through blast to get other crystal structures where your search sequence is conserved. Even though they are not sequence dependent, It is highly likely there is a pattern (in your known sequence) of amino acids which can make the fold. Did you try Zif-BASE $\endgroup$
    – Vasista
    Oct 28, 2021 at 8:00
  • $\begingroup$ @Vasista Do you think you could expand that into an answer? This question has remained in the unanswered queue for almost 3 months now! $\endgroup$
    – Nike Dattani
    Jan 14, 2022 at 2:01
  • $\begingroup$ It seems that @Vasista asked you in their last comment, about whether or not you tried Zif-BASE. I think without at an answer to that comment, your chances of getting an answer from Vasista would be lower than if you did answer the comment. Have you had a chance to try it yet? $\endgroup$
    – Nike Dattani
    Jan 27, 2022 at 0:37

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