The user can specify atom type for network construction, distance range (in Å) and minimal amino acid separation along the sequence. We have developed a web server for network based analysis of protein structures, NAPS, that facilitates quantitative and qualitative (visual) analysis of residue–residue interactions in: single chains, protein complex, modelled protein structures and trajectories (e.g. The network representation of proteins provide a systems approach to topological analysis of complex three-dimensional structures irrespective of secondary structure and fold type and provide insights into structure-function relationship. An alternative approach that has shown promise is modelling proteins as a network of non-covalent interactions between amino acid residues. Traditionally, protein structures have been analysed by the secondary structure architecture and fold arrangement.
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