Answers.Body: <p>After translation, proteins fold to achieve a specific 3D structure which allows them to perform their specific functions. The structure of a protein computationally inferred through energy minimization often corresponds quite well to that specific, real-life folded 3D structure.</p>
  <p>If you are interested in the exact reason why proteins tend to fold to a conformation of minimal energy (even though this is an oversimplification of what's really happening) you would have to dive a bit deeper into the thermodynamics of proteins: <a href="https://en.wikipedia.org/wiki/Protein_dynamics" rel="noreferrer">https://en.wikipedia.org/wiki/Protein_dynamics</a></p>
  <p><strong>TL;DR: Energy minimization is often used to get an idea of the protein's real-life conformation (i.e. structure) through computational means.</strong></p>
  
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Answers.Text: dont forget to add post-translational modification thought [i.e. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6779701/ ]
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Body: <ul>
  <li><a href="https://onlinelibrary.wiley.com/doi/10.1002/jcc.23330" rel="nofollow noreferrer">High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models</a></li>
  </ul>
  <p>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).</p>
  <p>This tool provides two options: conversion (1) with energy minimization, and (2) without energy minimization.</p>
  <ul>
  <li><a href="https://www.intechopen.com/chapters/74105" rel="nofollow noreferrer">Energy Minimization</a></li>
  </ul>
  <p>The above paper says that:</p>
  <blockquote>
  <p>...<br />
  The goal of energy Minimization is to find a set of coordinates representing the minimum energy conformation for the given structure.<br />
  ...<br />
  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.<br />
  ...</p>
  </blockquote>
  <p>I haven't understood the quote from the second paper.</p>
  <p>Why do we need to know the minimum energy conformation of a protein chain? I.e., why do we want to do <em>energy minimization</em>?</p>
  
Tags: <proteins><protein-structure><protein-protein-interaction>
Title: Why do we need to find minimum energy in a protein chain?
ThreadText: # Why do we need to find minimum energy in a protein chain?
  
  (Asked by: username_0 on 2022-11-21)
  
  * [High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models](https://onlinelibrary.wiley.com/doi/10.1002/jcc.23330)
  
  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.
  
  * [Energy Minimization](https://www.intechopen.com/chapters/74105)
  
  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*?
  
  **Tags:** proteins, protein-structure, protein-protein-interaction
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-11-21. Score: 6 | Accepted answer
  
  After translation, proteins fold to achieve a specific 3D structure which allows them to perform their specific functions. The structure of a protein computationally inferred through energy minimization often corresponds quite well to that specific, real-life folded 3D structure.
  
  If you are interested in the exact reason why proteins tend to fold to a conformation of minimal energy (even though this is an oversimplification of what's really happening) you would have to dive a bit deeper into the thermodynamics of proteins: <https://en.wikipedia.org/wiki/Protein_dynamics>
  
  **TL;DR: Energy minimization is often used to get an idea of the protein's real-life conformation (i.e. structure) through computational means.**
  
  > **Comments:**
  > **username_2**: dont forget to add post-translational modification thought [i.e. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6779701/ ]  
  
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