Version 1
: Received: 10 November 2023 / Approved: 13 November 2023 / Online: 14 November 2023 (17:02:04 CET)
How to cite:
Basu, S. Plot-Tools in Protein Structure Validations: From the Ramachandran Plot to the Complementarity Plot (Commentary). Preprints2023, 2023110741. https://doi.org/10.20944/preprints202311.0741.v1
Basu, S. Plot-Tools in Protein Structure Validations: From the Ramachandran Plot to the Complementarity Plot (Commentary). Preprints 2023, 2023110741. https://doi.org/10.20944/preprints202311.0741.v1
Basu, S. Plot-Tools in Protein Structure Validations: From the Ramachandran Plot to the Complementarity Plot (Commentary). Preprints2023, 2023110741. https://doi.org/10.20944/preprints202311.0741.v1
APA Style
Basu, S. (2023). Plot-Tools in Protein Structure Validations: From the Ramachandran Plot to the Complementarity Plot (Commentary). Preprints. https://doi.org/10.20944/preprints202311.0741.v1
Chicago/Turabian Style
Basu, S. 2023 "Plot-Tools in Protein Structure Validations: From the Ramachandran Plot to the Complementarity Plot (Commentary)" Preprints. https://doi.org/10.20944/preprints202311.0741.v1
Abstract
A picture is worth a thousand words. Many branches of Science have been historically benefited with plots and visual analyses (lately, image processing and deep learning) alongside with traditional number crunching. In Molecular Biophysics, one such problem is the structure validation problem in proteins which stands with a history of plot-tools being effectively serving the complex problem to its complete resolution. Spanning across six decades, validation of protein structures (from experimental to modeled) dates back to the legendary Ramachandran Plot (with its never ending growth and modern-day applications) to the relatively recent innovation of the Complementarity Plot (CP), establishing the dual nature of complementarity as the physical basis of both binding and folding of proteins. Lately, CP has been extended to serve as a trustworthy free energy predictor utilizing supervised learning in the form of a comprehensive web-server (EnCPdock: https://www.scinetmol.in/EnCPdock/) that can be directly used in the design of protein interfaces. The commentary recapitulate the history of structure validation with a special emphasis on plot tools, highlighting key features and important discoveries worth re-visiting.
Keywords
Proteins, Protein Science; Structure validation; Ramachandran Plot; Complementarity Plot
Subject
Biology and Life Sciences, Biophysics
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
