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      <h2>Integrated Methods, Tools and Databases</h2>
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        <h4>DSSP (hydrogen bond estimation algorithm)</h4>

        DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein.
        <ul>
          <li>Reference 1: http://www.ncbi.nlm.nih.gov/pubmed/6667333 (Kabsch and Sander)</li>
          <li>Reference 2: http://www.ncbi.nlm.nih.gov/pubmed/22877863 (BioJava)</li>
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      <h4>Modeller</h4>

      Modeller is a tool for homology modelling of protein structures.
      <ul>
        <li>Reference: https://www.ncbi.nlm.nih.gov/pubmed/24573470</li>
        <li>Homepage: https://salilab.org/modeller/</li>
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      <h4>Rosetta</h4>

      The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures.
      <ul>
        <li>Reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760476/</li>
        <li>Homepage: https://www.rosettacommons.org/software</li>
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      <h4>Elastic Network Models</h4>

      Elastic Network Models (ENMs) are applications of Normal Mode Analysis (NMA) aimed to predict protein motions from their crystallographic three-dimensional coordinates. The two models used in LoopGrafter are Gaussian (GNM) and Anisotropic (ANM), as implemented in ProDy. ANM produces a better prediction of the directionality of motions, and thus is better suited for cross-correlation analysis. 
      <ul>
        <li>Reference 1 (GNM): https://pubmed.ncbi.nlm.nih.gov/9218955/</li>
        <li>Reference 2 (ANM): https://pubmed.ncbi.nlm.nih.gov/16928735/</li>
        <li>Reference 3 (ProDy): https://pubmed.ncbi.nlm.nih.gov/24849577/</li>
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