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Related Experiment Video

Updated: Sep 20, 2025

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

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

Published on: July 16, 2017

Wenxiang 3.0: Evolutionary Visualization of α, π, and 3/10 Helices.

John R Jungck¹, Metehan Cebeci¹

¹Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.

Evolutionary Bioinformatics Online

|June 7, 2022

Summary

Wenxiang 3.0 enhances protein helix visualization by incorporating evolutionary conservation, diverse helix types (alpha, pi, 3/10), and amino acid physico-chemical properties into planar graph diagrams.

Keywords:

Wenxiang diagrams and 3/10 helices evolutionary conservation α π

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Published on: December 25, 2021

Area of Science:

Biochemistry
Structural Biology
Bioinformatics

Background:

Protein secondary structures, particularly helices, are fundamental to protein function.
Existing visualization methods like helical wheels have limitations in representing complex helical information.
Wenxiang diagrams offer a planar graph approach for visualizing protein helices.

Purpose of the Study:

To introduce Wenxiang 3.0, an upgraded version of the Wenxiang diagram tool.
To enhance the visualization of protein helices by integrating evolutionary and physico-chemical data.
To provide a more comprehensive tool for analyzing protein structure and sequence relationships.

Main Methods:

Development of Wenxiang 3.0 software with new features.
Integration of CONSURF encoding for evolutionary conservation visualization.
Implementation of arc overlays to represent pitches of alpha, pi, and 3/10 helices.
Mapping of amino acid physico-chemical properties to geometric shapes.

Main Results:

Wenxiang 3.0 allows coloring amino acid residues based on evolutionary conservation.
The software can now illustrate different helix types (alpha, pi, 3/10) using pitch arcs.
Physico-chemical properties are visually represented by colored geometric shapes for each residue.

Conclusions:

Wenxiang 3.0 offers a significantly enhanced method for visualizing protein helices.
The new features facilitate deeper insights into protein structure-function relationships.
This tool aids researchers in analyzing sequence-structure-evolutionary conservation correlations.