On Tue, Jun 30, 2009 at 2:24 PM, Buz Barstow <b...@mac.com> wrote:

> I have a very large library (almost 1000) of similar genetic
> sequences, for which I would like to generate homology models. Does
> anyone know of a way to automate requests to a homology modeling
> server, such as SWISS-Model through pymol, or alternatively through
> python?

I believe Modeller uses Python - never tried it myself, though.  There is a
server for Modeller but academic users can download the program itself.

There is in fact an API for using SWISS-Model from a Perl script (which
could probably be converted to Python, or wrapped by a Python script), which
I used years ago for a similar project.  As far as I know this is
unpublished, probably because they don't want people to trash their server,
but they were happy to supply it when I contacted the site maintainer.  They
asked that I limit the frequency of my requests, however.  I would recommend
emailing them.  (I have no idea how Modeller compares to SWISS-Model, but I
suspect it's more rigorous, especially when sequence homology is remote.)

There are other ways to go about this - bioinformaticists have been abusing
online databases and servers like this for years - but it's considered bad
etiquette to do this without permission (and some groups explicitly forbid
this use).

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