ScrewFit : combining localization and description of protein secondary structure
ScrewFit : combining localization and description of protein secondary structure
By Gerald Kneller, and Paolo Calligari
Acta Crystallographica Section D (2006)
Abstract Paper

Paolo  Calligari

Int. School for Advanced Studies Molecular and Statistical Biophysics

Italy

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A tri-peptide with two peptide bonds in the extended conformation, where the symbol R stands for a non-specified side-chains. The screw motion relating the yellow triangles formed by the O, C, N atoms of the peptide planes defines the local helix which is schematically represented by the cylinder and the corresponding screw arrow. The radius of the cylinder corresponds to the radius of the screw motion. At the same extent, the scalar product of the axis of two consecutive cylinders correspond to the straightness parameter.
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Abstract
A simple and efficient method is presented to describe the secondary structure of proteins in terms of orientational distances between consecutive peptide planes and local helix parameters. The method uses quaternion-based superposition fits of the protein peptide planes in conjunction with Chasles’ theorem, which states that any rigid-body displacement can be described by a screw motion. The helix parameters are derived from the best superposition of consecutive peptide planes and the ‘worst’ fit is used to define the orientational distance. Applications are shown for standard secondary-structure motifs of peptide chains for several proteins belonging to different fold classes and for a description of structural changes in lysozyme under hydrostatic pressure. In the latter case, published reference data obtained by X-ray crystallo- graphy and by structural NMR measurements are used.
Kneller, G., and P. Calligari, "ScrewFit : combining localization and description of protein secondary structure", Acta Crystallographica Section D , D62, 302–311.
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Please cite the publication as :

Kneller, G., and P. Calligari, "ScrewFit : combining localization and description of protein secondary structure", Acta Crystallographica Section D , D62, 302–311.

Please cite the companion website as :

Kneller, G., and P. Calligari, "ScrewFit : combining localization and description of protein secondary structure", RunMyCode companion website, http://www.execandshare.org/CompanionSite/Site385

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    ScrewFit : combining localization and description of protein secondary structure
    P. Calligari (2014)
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    • Paolo Calligari

      Int. School for Advanced Studies Molecular and Statistical Biophysics

      Italy

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