Re: [ccp4bb] 3D Structure Search

[Briggs, David C]

Also,


TopSearch https://topsearch.services.came.sbg.ac.at/

CAME - TopSearch :: Structure Search<https://topsearch.services.came.sbg.ac.at/>
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Sequence Analysis Highlight identical residues Jmol Mode HTML5 Java. Cite 
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Dave


==

Dr David C Briggs

Hohenester Lab

Department of Life Sciences

Imperial College London

UK

http://about.me/david_briggs


From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Daniel Rigden 
<drig...@liverpool.ac.uk>
Sent: 16 February 2018 08:29:29
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 3D Structure Search

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
>

--
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/
Crown St.,
Liverpool L69 7ZB, U.K.

Re: [ccp4bb] 3D Structure Search

[Daniel Rigden]

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



--
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/
Crown St.,
Liverpool L69 7ZB, U.K.

Re: [ccp4bb] 3D Structure Search

[Ethan A Merritt]

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

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] 3D Structure Search

[Tomas Malinauskas]

Dear Nicola,
PDBeFold is great too: http://www.ebi.ac.uk/msd-srv/ssm/
Best wishes,
Tomas

On Thu, Feb 15, 2018 at 11:16 PM, 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.
>
> Thanks in advance for your suggestions,
>
> Nicola

[ccp4bb] 3D Structure Search

[Nicola Evans]

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.

Thanks in advance for your suggestions,

Nicola