1. Predicting Allosteric Changes from Conformational Ensembles
Martin Zacharias 
Structure 
Volume 25, Issue 3, Pages (March 2017)
DOI: /j.str
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2. Figure 1 Conformational Ensemble Generation by Normal Mode Analysis
(A) Ensemble of pyruvate kinase structures found in the unit cell of the pdb1AQF structure (superimposed structures represented as colored cartoons). Ensembles of conformations can be generated computationally using distance geometry or normal mode analysis: (B) Superposition of pyruvate kinase structures generated by deforming along the softest lowest frequency normal mode calculated using an elastic network model (colored cartoon representation). The generated conformational ensemble can be influenced by bound ligands: (C) The ensemble generated in the presence of a ligand (van der Waals representation) reduces the global flexibility and limits the extension of the ensemble of possible states (compare superposition of ensembles in [B] and [C]).
In this issue of Structure, Greener et al. (2017) describe a new approach for calculating ensembles of protein conformations based on two experimental input structures (in contrast to the use of one structure in the normal mode-based approach illustrated in [B] and [C]). It allows the generation of ensembles that span apo and holo forms of protein structures and the prediction of allosteric sites in proteins.
Structure  , DOI: ( /j.str )
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