Visualizing alpha-helical peptides in R with helixvis

View Researcher's Other Codes

Disclaimer: The provided code links for this paper are external links. Science Nest has no responsibility for the accuracy, legality or content of these links. Also, by downloading this code(s), you agree to comply with the terms of use as set out by the author(s) of the code(s).

Authors Raoul R. Wadhwa, Vigneshwar Subramanian, Regina Stevens-Truss
Journal/Conference Name J. Open Source Software
Paper Category
Paper Abstract Studying the interactions of short peptides is conceptually non-trivial, even when the peptide’s primary and secondary structures are known. The difficulty is often a result of the three-dimensional spatial complexity present in protein secondary structure. Here, we focus on α-helical secondary structure. Two-dimensional visualizations, specifically helical wheels (Figure 1, left panel) and wenxiang diagrams (Figure 1, right panel), are used by biochemists to study α-helices. Helical wheels provide a bird’s eye view of a helical peptide with the amino acids forming a perfect circle, and allow for rapid identification of the peptide’s hydrophobic faces (Schiffer & Edmundson, 1967), helping solve a common challenge in biochemistry research. In contrast, wenxiang diagrams incorporate residue order by making residue distance from the center directly proportional to residue position in the peptide (Chou, Zhang, & Maggiora, 1997). However, this makes the identification of hydrophobic faces less intuitive. Together, these two forms of visualization allow researchers to more clearly understand the underlying structure of α-helical peptides. Given the existence of databases listing thousands of peptides, all of which need to be visualized for manual inspection prior to wet-lab experiments, there is a need for software that allows for rapid programmatic construction of large numbers of publication-quality helical wheels and wenxiang diagrams.
Date of publication 2018
Code Programming Language R

Copyright Researcher 2022