Allostery is the process by which action at one site, such as the binding of an effector molecule, causes a functional effect at a distant site. Allosteric mechanisms are important for the regulation of cellular processes, altering the activity of a protein, or the whole biosynthetic pathway. Triggers for allosteric action include binding of small molecules, protein-protein interaction, phosphorylation events and modification of disulphide bonds. These triggers can lead to changes in accessibility of the active site, through large or small motions, such as hinge motion between two domains, or the motion of a single side chain.One way to consider allostery is as signal propagation from one site to another, as a change in residue to residue contacts. Networks provide a way to represent these changes. Daily et al  introduce the idea of contact rearrangement networks, constructed from a local comparison of the protein structure with and without molecules bound to the allosteric site. These are referred to as the active and inactive structures respectively. To measure the whether a residue to residue contact is changed between the active and inactive states, the authors use a rearrangement factor (R(i,j)). This is the ratio of atoms which are within a threshold distance (5 angstroms) in only one of the active or inactive states (whichever is greater), to the total number of atoms in the two residues.The rearrangement factor is distributed such that the large majority of residues have low rearrangement factors (as they do not change between the active and inactive state). To consider when a rearrangement is significant the authors use a benchmark set of non allosteric proteins to set a threshold for the rearrangement factor. The residues above this threshold form the contact rearrangement network, which can be analysed to assess whether the allosteric and functional sites are linked by residue to residue contacts. In the paper 5/15 proteins analysed are found to have linked functional and allosteric sites. Collective rigid body domain motion was not initially analysed by these contact rearrangement networks, however a later paper , discusses how considering these motions alongside the contact rearrangement networks can lead to a detection of allosteric activity in a greater number of proteins analysed. These contact rearrangement networks provide a way to assess the residues that are likely to be involved in allosteric signal propagation. However this requires a classification of allosteric and non-allosteric proteins, to undertake the thresholding for significance of the change in contacts, as well as multiple structures that have and do not have a allosteric effector molecule bound. Alternatively, Van den Bedem et al  define contact networks of conformationally coupled residues, in which movement of an alternative conformation of a residue likely influences the conformations of all other residues in the contact network. They utilise qFit, a tool for exploring conformational heterogeneity in a single electron density map of a protein, by fitting alternate conformations to the electron density. For each conformation of a residue, it assesses whether it is possible to reduce steric clashes with another residue, by changing conformations. If a switch in conformations reduces steric clashes, then a pathway is extend to the neighbours of the residue that is moved. This continued until no new clashes are introduced. Pathways that share common members are considered as conformationally coupled, and grouped into a single contact network. As this technique is suitable for a single structure, it is possible to estimate residues which may be involved in allosteric signalling without prior knowledge of the allosteric binding region.
These techniques show two different ways to locate and annotate local conformational changes in a protein, and determine how they may be linked to one another. Considering whether these, and similar techniques highlight the same allosteric networks within proteins will be important in the integration of many data types and sources to inform the detection of allostery. Furthermore, the ability to compare networks, for example finding common motifs, will be important as the development of techniques such as fragment based drug discovery present crystal structures with many differently bound fragments.
 Daily, M. D., Upadhyaya, T. J., & Gray, J. J. (2008). Contact rearrangements form coupled networks from local motions in allosteric proteins. Proteins: Structure, Function and Genetics. http://doi.org/10.1002/prot.21800
 Daily, M. D., & Gray, J. J. (2009). Allosteric communication occurs via networks of tertiary and quaternary motions in proteins. PLoS Computational Biology. http://doi.org/10.1371/journal.pcbi.1000293
 van den Bedem, H., Bhabha, G., Yang, K., Wright, P. E., & Fraser, J. S. (2013). Automated identification of functional dynamic contact networks from X-ray crystallography. Nature Methods, 10(9), 896–902. http://doi.org/10.1038/nmeth.2592