Fwd: [Bio-www] Protein diameter

Dan Bolser via bio-www%40net.bio.net (by dmb from bioinformatics.org)
Tue Jan 27 04:17:33 EST 2009


BIOSCI blacklist (yw-out-1718.google.com ) ?

---------- Forwarded message ----------
From: Dan Bolser <dan.bolser from gmail.com>
Date: 2009/1/27
Subject: Re: [Bio-www] Protein diameter
To: Benjamin Walter <benwalter44 from gmail.com>
Cc: bio-www from magpie.bio.indiana.edu


Interesting question.

you could look at the bounding box which is a diameter by some
definition. However, most people use the radius of gyration, which is
actually a measure of how compact the protein is.

There have been lots of studies on protein density.

HTH,
Dan.

2009/1/26 Benjamin Walter <benwalter44 from gmail.com>:
> Dear friends
>
> I would like to ask whether there is some way to measure the diameter of a
> molecule (its longest diameter).  (On protein database or the like web
> site).
> One way (on Jmol viewer) is to measure a distance between two extremeties of
> a given protein.
> However, this method is subject to chance of missing the longest diameter.
> Could you please help?
>
> Best regards,
> Ben
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