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Wenxiang 3.0

Author(s): John R Jungck1, Metehan Cebeci2

1. Interdisciplinary Science Learning Center at the University of Delaware 2. University of Delaware

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Summary:
Wenxiang diagrams illustrate protein helices as spirals on a plane and thus have the advantage over helical wheels of being planar graphs. Wenxiang 3.0 extends the original version by adding three major features: (1) individual amino acid residues…

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Wenxiang diagrams illustrate protein helices as spirals on a plane and thus have the advantage over helical wheels of being planar graphs. Wenxiang 3.0 extends the original version by adding three major features: (1) individual amino acid residues can be colored according to their evolutionary conservation in comparative multiple sequence alignments using CONSURF encoding; (2) α, π, and 3/10 helices can be illustrated by overlaying arcs representative of the pitches of these helices; and, (3) the physico-chemical properties of amino acids residues in the protein sequence can be re- presented by colored geometric shapes.

Description

The file titled "Wenxiang 3" contains all the software needed to make Wenxiang diagrams with a user interface, while the file titled "Wenxiang 3 No User Interface" does not have a user interface, and instead contains an example of how to run the software without the interface.

Notes

This software is built on top of an R package originally built by Raoul R. Wadhwa, Vigneshwar Subramanian, and Regina Stevens-Truss:

Wadhwa, R. R., Subramanian, V., & Stevens-Truss, R. (2018). Visualizing alpha-helical peptides in R with helixvis. Journal of Open Source Software, 3(31), 1008.

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