IISc GraProStr
This web-tool converts protein structures into networks/ graphs with amino acids as nodes and the noncovalent interactions among them as edges. The edges are drawn on the basis of the number of atom-atom contacts (defined asInteraction Strength)between the amino acids or on the basis of Cα-Cα/Cβ-Cβ distances.

The connectivity(adjacency) matrix thus generated is used to calculate an array of graph/network parameters such are clusters, hubs, cliques and communities. The matrix can also be represented pictorially using GraphViz.

For details please refer to the papers below.

Protein Structure Networks

(If you are unaware of the words like graphs, networks, nodes and edges please browse through this Wikipedia Link)

Protein Side-chain Graphs/Networks (PScN) makes use of Interaction Strength to define edges. The Interaction Strength ranges from 0% (atleast 1 atom-atom contact) to as high as 20%. The recommended values are in the range of 4% to 10% for strong interactions (smaller clusters) and 0% to 2% for weak interactions (connections at the domain levels). Cliques and communities are generally evaluated at 2% to 4%.
This tool is primarily for evalulating the interactions within the proteins (both monomers and multimers).

If you like to include the ligands/heteroatoms in your calculation then use Protein Ligand Graphs/Networks (PLN) module. This tool considers any heteroatom in the pdb as a ligand. It uses interaction strength to calculate inter-residues edges. Additionally, it draws an edge between an amino-acid and the ligand if there exists atleast one atom of the amino acid within 4.5Ả of any ligand atom.

CαProtein Backbone Graphs/Networks (PBN) utilizes inter-residue Cα- Cα distances to generate structure graphs.

Similarly, Cβ Protein Structure Graphs/Networks utilize inter-residue Cβ- Cβ distances to generate structure graphs.

If you want some hands on training, please check our tutorials page.

Contributors

Project Coordinator: Prof. Saraswathi Vishveshwara
N. Kannan, Swarna Mayee Patra, Rakesh Kumar Pandey, N. Sanjeev, K.V. Brinda, R.Sathyapriya, Amit Ghosh, Vijay and Vidya Niranjan

Citation

Vijayabaskar, M. S.; Niranjan, Vidya; Vishveshwara, Saraswathi, Open Bioinformatics Journal;2011, Vol. 5 Issue 2011, p53

Contact Us

saraswathi@iisc.ac.in