The above research paper is about a software tool for reconstructing a protein's main chain model only from its alpha-carbon backbone (aka, C-alpha trace).

This tool provides two options: conversion (1) with energy minimization, and (2) without energy minimization.

The above paper says that:

The goal of energy Minimization is to find a set of coordinates representing the minimum energy conformation for the given structure.
In molecular modeling we tend to are particularly curious about minimum points on the energy surface. Minimum energy arrangements of the atoms correspond to stable states of the system; any movement off from a minimum provides a configuration with a better energy.

I haven't understood the quote from the second paper.

Why do we need to know the minimum energy conformation of a protein chain? I.e., why do we want to do energy minimization?

  • 2
    $\begingroup$ The energy minimization is not only used for protein. If you want to calculate any property of your system (and want that property to persist), then you calculate it the minimal energy structure: minimum of potential energy surface. I think that in 2, there is a typo: instead of better, could be greater. $\endgroup$
    – Camps
    Oct 20, 2022 at 13:08
  • $\begingroup$ @Camps, I think that in 2, there is a typo: instead of better, could be greater. --- This is exactly what is written in the paper. $\endgroup$
    – user366312
    Oct 20, 2022 at 13:17
  • $\begingroup$ I am not questioning what you wrote. My thought is that papers are not perfect, even after a proofreading, so, maybe that is an error. $\endgroup$
    – Camps
    Oct 20, 2022 at 14:04
  • $\begingroup$ Cross posted on Bioinformatics SE $\endgroup$
    – Tyberius
    Nov 21, 2022 at 21:33
  • $\begingroup$ @Tyberius, Yes, because this question is a month old, and no answer posted. $\endgroup$
    – user366312
    Nov 21, 2022 at 22:12

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