Aminonet-a tool to construct and visualize amino acid networks, and to calculate topological parameters
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Cites methods from "Aminonet-a tool to construct and vi..."
...For e.g., Aminonet provides network based analysis of physico-chemical properties of amino acids (Aftabuddin and Kundu, 2010) while GraProStr (M S Vijayabaskar et al., 2011) allows identification of hubs, cluster of residues, cliques and modularity based analysis....
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...The user can either provide a PDB ID or upload a structure file in PDB format as input (PDB is the Protein Data Bank; Berman et al., 2000)....
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...Furthermore, not all crystallographic asymmetric units contain a biologically relevant oligomeric assembly and a server like PISA (Krissinel & Henrick, 2007) can be used to extract the coordinates of the relevant complex (assembly)....
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"Aminonet-a tool to construct and vi..." refers background in this paper
...Network theory has been recognized as a very powerful tool to understand and characterize several complex systems and their individual components (Barabasi & Oltavi, 2004; Dorogovtsev & Mendes, 2003)....
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