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Newman Projections

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Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
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Related Experiment Video

Updated: Apr 26, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

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.

|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.

Keywords:

Fourier transform Wigner-D functions computational methods correlation value protein classification protein structure reciprocal space root-mean-square deviation similarity value tubulin

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Last Updated: Apr 26, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Published on: July 16, 2017

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

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.