Sym-Bio GUI: A graphical user interface to analyze protein aminoacid residue contact networks
Alessandro Giuliani, Luisa Di Paola, Valentina Russo · 2012
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.