1. What is a Clique?

In the mathematical area of graph theory, a clique in an undirected graph is a subset of its vertices such that every two vertices in the subset are connected by an edge. Cliques are one of the basic concepts of graph theory and are used in many other mathematical problems and constructions on graphs.

2. What are Hubs?

Hubs are highly connected nodes in the network.In packing based protein structure network(PSN) studies a node is declared a hub if its degree is atleast 4.

3. What are Communities?

A community is defined as a union of smaller K-cliques(a set of K nodes in which each node is connected to all the other nodes) that share node/s.

4. What is the importance of finding largest cluster?

It gives us the idea regarding the compactness in the structure of the protein.Also It also helps us to compare the native protein with its decoy ones.

5. What does the Cut Off value signifies?

It signifies the minimal interaction strength the tool will take for clustering

6 . What is a Clean PDB? Do we need to supply a clean PDB or a normal PDB structure?

The clean PDB is error free PDB due to naming convention and other reasons. The tool takes care to some level for cleaning the PDB. However the users are encouraged to input a clean PDB

7. How to interpret the graphical result? Can it be exported to mail account?

The results to be analysed are explained in tutorials section (http://vishgraph.mbu.iisc.ernet.in/GraProtS/tuts.html). No it can not be sent through mail, User can download in from the tool.

8. An outline flowchat of the work?