PDB2Graph

System’s perspective to protein structure prepared by 2D graphic visualization next to traditional molecular perspective available by 3D molecular graphic methods provide a deep concept in protein structure-function relationship and used to explain many challenging problems in today structural biology as analyzing protein stability, folding, allosteric communication, enzyme catalysis or mutation effect prediction.

PDB2Graph is a Matlab-based interface for protein structure network (PSN) construction, visualization and analysis. In this interactive and user-friendly interface, PDB serves as input. The output is an undirected coarse-grained distance-based graph which can be exported in standard graph formats of popular packages like Cytoscape (.sif), Pajek (.net) and UCINET (.dl) which allows users to perform complementary analysis by other packages. In analysis section, two kinds of information can be retrieved. statistical measurements and topological-global feature calculation is available via the Analysis menu and In the “Advanced Analysis” section, some centrality indicators with high correlation to protein structural and functional properties are calculated containing characteristic path length, closeness, betweenness,  clustering coefficient and degree distribution.

PDB2Graph offers a complementary graphical toolbox with high quality visualization of graphs as well as being easy-to-use enough and user-friendly for applicants without programming expertise. This toolbox gives a guideline to select proper amino acids for mutagenesis-based methods in protein engineering.

Download :

MATLAB source code

User guide 

 

 

 

 

Reference:

* Niloofar Niknam, Hamed Khakzad, Seyed Shahriar Arab, Hossein Naderi-Manesh (2016) PDB2Graph: A Toolbox for Identifying Critical Amino Acids Map in Proteins Based on Graph Theory. Computers in Biology and Medicine  Vol. 72,  151–159.   doi: 10.1016/j.compbiomed.2016.03.012