Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

Background: An elastic network model is proposed for the interactions between closely (less than or equal to 7.0 Angstrom) located alpha-carbon pairs in folded proteins, A single-parameter harmonic potential is adopted for the fluctuations of residues about their mean positions in the crystal structure, The model is based on writing the Kirchhoff adjacency matrix for a protein defining the proximity of residues in space, The elements of the inverse of the Kirchhoff matrix give directly the auto-correlations or cross-correlations of atomic fluctuations.