Inhibitor binding alters the directions of motions in HIV-1 reverse transcriptase

"Anisotropy of fluctuation dynamics of proteins with an elastic network model" Atilgan, AR, Durrell, SR, Jernigan, RL, Demirel, MC, Keskin, O. & Bahar, I. Biophys. J. 80, 505-515, 2001. (.pdf)

 Anisotropic Network Model (Atilgan et al., 2001)

• The anisotropic network model (ANM) is an extension of the GNM to the 3N-d space of collective modes.
  

• The inter-residue 'distances' are controlled by harmonic potentials in the GNM, ANM adopts further assumption that the three (-x, -y and -z) components of the inter-residue separation vectors obey Gaussian dynamics.
  

• G is replaced by its 3N x 3N counterpart (1/g)H where H is the Hessian matrix of the second derivatives of the intermolecular potential V = (g/2) DR^T G DR.
  

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