Sym-Bio GUI: A graphical user interface to analyze protein aminoacid residue contact networks

Proteomics impact on drug design strongly relies on the availability of fast and efficient tools to analyze protein structures. Within this framework, a promising approach deals with the topological analysis of between-residue contact networks. In this paper, we present SymBio, a tool modelled via two Graphical User Interfaces (GUI), aimed at translating the 3D structure of the target protein, fed in the standard PDB format, into an adjacency list, formatted in a custom fashion (NWB file), that is further transmitted to a Network Analysis Toolkit (NAT), and an adjacency matrix for the dedicated clustering analysis. Both classical network invariants (computed by NAT) and a clustering procedure of the nodes (computed by GUI´s), provide potentially relevant topological information at both single residue and entire structure levels.