Another topology-independent method is CLICK, available as a server here
http://cospi.iiserpune.ac.in/click/
You might also want to try FATCAT which considers potential flexibility
of separate subdomains in its structural alignment
http://fatcat.burnham.org/fatcat-cgi/cgi/fatcat.pl?-func=search
Dan
On 15/02/18 23:25, Ethan A Merritt wrote:
On Thursday, February 15, 2018 3:16:50 PM PST Nicola Evans wrote:
I have recently solved a novel structure which previously did not have any
structural homologues (as related by sequence identity). I was wondering if
anyone could recommend a 3D structural search engine? I used the Dali server
which has been recommended to me in the past (and with past success) but the
top few hits this time aren't similar structurally (although I haven't
exhausted the list yet). I just want to confirm if the folds are truly novel or
not.
Dali is sensitive to the order of secondary structure elements.
This is relevant if you are looking for evolutionary relatedness, but
not if you just want to ask "does it look like this".
For the latter question, I suggest the VAST server at NCBI.
https://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml
Ethan
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Dr Daniel John Rigden Tel:(+44) 151 795 4467
Institute of Integrative Biology FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool http://pcwww.liverpool.ac.uk/~drigden/
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