Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis
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Structure of HIV-1 Capsid Assemblies by Cryo-electron Microscopy and Iterative Helical Real-space Reconstruction
Published on: August 9, 2011
H Sklenar1, C Etchebest, R Lavery
1Central Institute of Molecular Biology, Academy of Sciences of the GDR, Berlin Buch.
Abstract:
We present a general and mathematically rigorous algorithm which allows the helicoidal structure of a protein to be calculated starting from the atomic coordinates of its peptide backbone. This algorithm yields a unique curved axis which quantifies the folding of the backbone and a full set of helicoidal parameters describing the location of each peptide unit. The parameters obtained form a complete and independent set and can therefore be used for analyzing, comparing, or reconstructing protein backbone geometry. This algorithm has been implemented in a computer program named P-Curve. Several examples of its possible applications are discussed.
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