Re: CCL:Alpha Helix kink

 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,
 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%
 Phone: +1 (650) 725-6497
 Fax : +1 (650) 725-8021