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?