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

Mike Marchywka marchywka at hotmail.com
Mon Mar 31 20:43:41 EDT 2008

I've used the Protein3dfit link from here ,


but it seems to be down right now. One suggestion I would make, however, is to
offer an API and not just a web interface. I have a script to use the above link
so I can submit files from a command line ( and integrate into automated stuff)
and I imagine your form could be reverse engineered too. Trying to reverse engineer
html is always annoying and it would probably be easier for you to write your web pages
on top of a documented stable API. Whlie the interactive java viwer may not make much sense
in this usage situation, your do offer pdf and pdb downloads that could be automated-
if there is really something in the pdf that is not in the pdb, text format may be easier although
certainly the pdb file is quite usable for automated analysis.

Mike Marchywka
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here. Thanks.

> From: Sterten at aol.com
> Date: Mon, 31 Mar 2008 16:35:07 -0400
> To: bbb at bioinformatics.org
> Subject: Re: [BiO BB] TopMatch protein structure alignment and superposition web service
> is it faster or better than MAFFT, which I use currently ?
> http://align.bmr.kyushu-u.ac.jp/mafft/online/server/
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