Dear Norbert,
The structure search functionality at RCSB.org should help find AB
complexes similar to yours:
1. Go to https://www.rcsb.org/search/advanced
2. In the "Structure Similarity" section, select "File upload" (using
the pull-down menu that has "Entry ID" as the default)
3. Upload the coordinate file for your complex
4. Select "Search for" = "Assemblies"
This should give you any assemblies in the PDB that have a globally
similar shape to your AB complex.
It will not give you locally similar matches (e.g. only one chain is
similar or only a subdomain of each chain is similar) nor super
assemblies (e.g. ABC where only AB is similar).
Please feel to let us know at i...@rcsb.org if you have any questions.
Sincerely,
Rachel Green
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On 1/29/2024 6:03 AM, Norbert Straeter wrote:
Dear all,
I have a heterodimeric complex AB and want to know if there are
similar complexes between homologs of A and homologs of B or even any
complex structures between such homologs. For the latter task, I could
search for homologs of A and homologs of B by advanced PDB search or
DALI etc. and next look for common PDB ids. Does anybody know a
program or website that is dedicated to this kind of job?
Best regards,
Norbert
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