Structural protein similarity program

Michel Leroux mleroux at unixg.ubc.ca
Thu Jan 5 12:08:39 EST 1995

In article <D1vt6z.CvJ at wst.edvz.sbg.ac.at>, floeckn at wst.edvz.sbg.ac.at
(Floeckner Hannes) wrote:

> Hi!
> I'm looking for public domain programs for structure-structure alignments and
> for the identification of structural similarities in protein folds. The
> program should run on either SGI or Dec-Alpha (in the worst case on
> MS-DOS PC's).
> Anyone who knows a program to do structure-strucutre alignment?
> Thanx
>         Hannes

Yes, I know of a program which may be just what you're looking for. It's
called PHD, and its purpose is to predict the secondary structure of any
given protein, and it also takes into account other similar (homologous)
protein sequences. The more sequences it can compare to from the protein
database, the better the prediction. They give a reference which claims
the prediction is about 70% accurate. I have recently used it and found
that the predicted GroEL secondary structure is VERY similar to the known
secondary structure of this protein.

It's available on any platform, and is very easy to use because it's a
free e-mail service. All you need to do is send the following e-mail

To: PredictProtein at embl-heidelberg.de

your name
your address

your e-mail address

predict secondary structure

# protein_name

MAFGIHRTIPECV...(etc., your protein sequence)

You receive a confirmation of your request promptly, and then about half
an hour later you get the secondary structure prediction. In your case,
you'd have to compare the secondary structures manually, but this should
serve your needs adequately.

Michel Leroux
mleroux at unixg.ubc.ca

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