Elastic Network Model — Protein Normal Modes

The Elastic Network Model (Tirion 1996; Bahar et al 1997) represents a protein as a network of C_α atoms connected by springs within cutoff r_c. The Kirchhoff matrix Γ: Γ_ij = −1 if d_ij < r_c, Γ_ii = Σ_j Γ_ij. Normal modes are eigenvectors of Γ; the lowest non-trivial modes describe large-scale hinge/breathing motions. B-factors ∝ (kT/γ)·[Γ⁻¹]_ii. Residue displacements show how each mode deforms the protein.