Using the Girvan–Newman (GN) algorithm ( Girvan and Newman, 2002), networks are divided into disjoint subnetworks called communities in which nodes have stronger and more connections to other nodes within the same community than they have to those outside the community. These communities, which can contain both amino acids and nucleotides, are similar to structural domains but are defined by the dynamics of the biomolecules (see Fig. A more detailed explanation of the network concepts and their associated algorithms as applied to dynamic networks is available in Sethi et al. Once the physical network of nodes and weighted edges is generated by the program networkSetup, both optimal and suboptimal paths are calculated by subopt, and the edge betweenness and community structure are determined by gncommunities. NetworkView simplifies the viewing of the above network properties superimposed onto large biomolecular complexes. VMD is available for Windows, MacOS X and Linux/UNIX. NetworkView is implemented as a Tcl plugin to VMD, which allows direct access to VMD’s powerful atomselection language and wrapper procedures for the creation and display of OpenGL objects. A graphical user interface with access to the most commonly used features in NetworkView is available through the VMD menu system: Extensions/Analysis/NetworkView. Three different types of data files can be loaded into NetworkView: network, community and suboptimal path. The data files are ASCII text and were designed to be human readable. These files can be generated by the programs networkSetup, gncommunities and subopt. ![]() NetworkView is not technically tied to these programs, however, so it can be used to visualize and analyze network data generated by other means. NetworkView provides an application programming interface (API) for selecting nodes and edges and then viewing the values associated with them. Documentation for the NetworkView API is available on the web at. ![]() A detailed introduction to the use of NetworkView has been provided in a tutorial with data files hosted at the same location. The necessary data files can be generated from MD trajectories or from PDB structures.
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