Subject: Re: CCL:Alpha Helix kink

From: Xavier Deupi <Xavier.Deupi %x% stanford.edu>
Date: Fri, 17 Jun 2005 10:18:42 -0700

Hi Mireille,

You can also use HelAnal (Bansal et al. J Biomol Struct Dyn. 2000 
Apr;17(5):811-9) to detect and measure local distortions of the helical 
structure, in terms of local (i.e. per residue) bend and twist angles. 
You can see an application to Pro-kinked alpha-helices in Deupi et al., 
Biophys J. 2004 Jan;86(1 Pt 1):105-15.

Hope this helps,

xavi

Mireille Krier wrote:

> Dear CCLers,
>
> we are looking for a tool that can detect (because not always induced 
> by proline)
> and measure the angle of an kink in an alpha helix.
> Any suggestions?
> We found in the literature SWINK, (Cordes et al., Sansom Group)
> was developed to estimate the kink and swivel angle of TM small alpha, 
> Greek-helices.
> Any ideas, if this is available?
>
> Many thanks in advance to the community for the any help provided.
>
> Mireille Krier
>

-- 
Xavier Deupi, Ph.D.
Department of Molecular and Cellular Physiology
Beckman Center for Molecular and Genetic Medicine (B161)
279 Campus Drive, Stanford University School of Medicine
Stanford, CA 94305 (USA)

E-mail: Xavier.Deupi %x% stanford.edu
Phone: +1 (650) 725-6497
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