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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
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Geometrical comparison of two protein structures using Wigner-D functions
S M Saberi Fathi1, Diana T White, Jack A Tuszynski
1Department of Physics, Ferdowsi University of Mashhad, Mashhad, Iran.
Proteins
|July 22, 2014
Summary
This study introduces a novel quantitative method to compare protein structures, even those with varying atom counts. The new "similarity value" offers a robust way to assess protein structural relationships.
Area of Science:
- Structural biology
- Biophysics
- Computational chemistry
Background:
- Comparing protein structures is crucial for understanding function and evolution.
- Existing methods often struggle with proteins of different sizes or complexities.
Purpose of the Study:
- To develop a quantitative and versatile method for comparing arbitrary protein structures.
- To introduce a new metric, the 'similarity value', for structural comparison.
Main Methods:
- Utilizing root-mean-square deviation (RMSD) for structural characterization.
- Employing a series expansion of the protein's shape function using Wigner-D functions.
- Demonstrating that expansion coefficients relate to structure factors.
Main Results:
- A novel 'similarity value' criterion for protein structure comparison was established.
- The method effectively handles proteins with differing numbers of atoms.
- Expansion coefficients were shown to correspond to structure factors.
Conclusions:
- The Wigner-D function expansion provides a robust framework for quantitative protein structure comparison.
- This method offers a solution for comparing proteins of varying sizes, advancing structural bioinformatics.
Keywords:
Fourier transformWigner-D functionscomputational methodscorrelation valueprotein classificationprotein structurereciprocal spaceroot-mean-square deviationsimilarity valuetubulinMore Related Videos
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