Protein Ligand Graph
PDB to retrieve
four letter alpha numeric code provided by RCSB PDB data bank eg: 1ask
PDB to Upload
Browse a pdb file from your computer
Cut Off (I
min
)
Minimal Interaction Strength (Optimal value: 4% - 7% for clusters, 2% - 5% for hubs and 1% - 3% for cliques and communities
%
Network Parameters
Clusters
Connected components in the graph
Monomeric clusters
Clusters in the monomers ( Multimers will display non-interface clusters )
Interface clusters
Interface cluster in multimers
Complete clusters
Monomeric clusters + complete clusters
Hubs
Highly connected residues in structure network
Monomeric Hubs
Hubs in the monomers ( Multimers will display non-interface Hubs )
Interface Hubs
Interface Hubs in multimers
Complete Hubs
Monomeric Hubs + Interface Hubs
Cliques
Rigid subgraphs ie., cliques with 'n' nodes and n(n-1) edges
Monomeric Cliques
Cliques in the monomers ( Multimers will display non-interface Cliques )
Interface Cliques
Interface Cliques in multimers
Complete Cliques
Monomeric cliques + Interface cliques
Communities
Connected components in the graph
Communities
Collection of cliques
Graphical Display
Image Display( can be saved as png)
GraphViz
Visualization of network using Graphviz
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