[BiO BB] TopMatch protein structure alignment and superposition web service

[Mike Marchywka]

> For each protein deposited in PDB, you can easily explore its structural neighborhood and visualize structural similarities with TopMatch.
> If you try with the example you mentioned, you find the dehydrosqualene synthase structures assigned to be similar to 1ezf.


Sure, if you have suspects I guess this is helpful. I was thinking of something like a cavity or surface database
however. I guess in this case, you could suspect functional similarities but I don't know if there is something
to compare shape and chemical environments of cavities. I wrote some cavity code for my home-made
molecule viewer and was able to generate some nice pictures by coloring cavity walls based on
nearest atom type, but I'm not sure if something like that would be useful for finding related enzymes.

I'll have to get the sequences and see if my rule annotater can find functional similarities in 1D when I 
get a chance. Are there known, conserved functional groups in 1D that help create the 3D structure even if
this amounts to limited total sequence identity?





> Date: Wed, 2 Apr 2008 10:52:07 +0200
> From: markii at came.sbg.ac.at
> To: bbb at bioinformatics.org
> Subject: Re: [BiO BB] TopMatch protein structure alignment and superposition web service
>
> Hi Mike,
>
> thanks for pointing to this interesting test case.
>
> Indeed, the structural similarity of dehydrosqualene synthase (PDB codes: 2zco, 2zcp, 2zcq, 2zcr, 2czs) and humane squalene synthase (PDB codes 1ezf) is striking in the view of their low sequence identity. TopMatch-web yields an RMS of 3.5A and a sequence identity of 11% if the respective chains A are compared.
>
> Talking about finding such similarities: one tool that is really helpful for this task is the qCOPS web service (some advertising again ;-) at
> http://navi.services.came.sbg.ac.at/bin/qCOPS.html
>
> For each protein deposited in PDB, you can easily explore its structural neighborhood and visualize structural similarities with TopMatch.
> If you try with the example you mentioned, you find the dehydrosqualene synthase structures assigned to be similar to 1ezf.
>
> For further information on qCOPS, see
> Sippl et al.
> A Discrete View on Fold Space
> Bioinformatics, 24, pp. 870-871 (2008)
> (Open Access: http://bioinformatics.oxfordjournals.org/cgi/reprint/btn020?ijkey=7zgnEsdKQIEfrN7&keytype=ref)
>
> Best regards,
> -Markus
>

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