System Requirements
The portal is browser independent and needs no added plugins to be installed in the browser.
The network visualization is performed using WebGL which is present in all modern browsers. Some of the popular browsers with WebGL are:
Firefox Mozilla: Version 4.0 and above.
Google Chrome: Version 9 and above.
Safari: Safari 6.0 and newer versions installed on OS X Mountain Lion, Mac OS X Lion and Safari 5.1 on Mac OS X Snow Leopard
If your browser version falls in the above range and still you are getting WebGL failure alert, then WebGL is supported by your browser but is disabled. Please enable it manually.
NAPS home page
PDB: Provide the PDB id or upload PDB file.
Analyze (analysis type): Determines the type of analysis to be performed. One of the following options can be selected:
Single chain: Analyze protein represented by one chain in PDB file.
Two chains: Analyze two proteins (protein complex) represented by two different chains in PDB file.
Chain: Chain id of PDB file which represents the desired protein. In case of analysis of protein complex, Chain 1 and Chain 2 represent the two proteins in complex. The chain field is case sensitive, i.e. 'A' is considered different from 'a'.
Graph type
C-alpha: An amino acid residue represented by the C-alpha atom is considered as node in the network
and an edge is constructed if the distance between the C-alpha atoms is less than the threshold defined by the user.
The default threshold is 7 Å.
C-beta: An amino acid residue represented by the C-beta atom is considered as node in the network
and an edge is constructed if the distance between the C-beta atoms (C-alpha for GLY) is less than the threshold defined by
the user. The default threshold is 7 Å.
Atom pair contact: An amino acid residue represented by the centre of residue is considered as node
in the network and an edge is constructed if the distance between any pair of atoms of the residue pair is less than
the threshold defined by the user. The default threshold is 5 Å.
Centroid (centre of mass): An amino acid residue represented by the centre of mass (centroid) of the
side chain is considered as node in the network and an edge is constructed if the distance between centroids is less than the
threshold defined by the user. The default threshold is 8.5 Å.
Interaction strength:An amino acid residue is considered as node in the network and an edge is
constructed if the interaction strength between two residues is more than the threshold defined by the user.
The default threshold is 4%.
Weight:
Unweighted: No weight is assigned to the edges. All edges are considered equally important.
Weighted: Weights are assigned to the edges depending on different criteria for different network types:
a) C-alpha:
Inverse of distance between C-alpha atoms.
b) C-beta:
Inverse of distance between C-beta atoms.
c) Any atom:
Number of atom pairs within threshold distance.
d) Centroid:
Inverse of distance between centre of mass of the residues.
e) Interaction strength:
Interaction strength between the residues.
Threshold: The lower and higher cutoff distance (in Å) determines the
range of distance to be considered for the construction of an edge between a pair of nodes (residues).
For "Interaction strength" (IS) type network, only the lower bound interaction strength (in %) is taken as input.
An edge is constructed if the interaction strength is greater than the given threshold.
Residue separation: Minimum separation of residues in the protein
sequence to be considered for network construction. A value in the range 1-15 can be selected.
Top menu
Description of options available at the Top Menu Bar.
Home: Link to the home page of the portal.
View: Link to the visualization page with network and structure representation.
Analysis: Options for all the analysis that can be performed on the network.
Properties: Link to global properties of the network.
Node Centrality: Link to node centrality analysis.
Edge Centrality: Link to edge centrality analysis.
Shortest path: Link to shortest path analysis.
k-clique: Link to k-clique analysis.
Domain view: Link to Multi-domain analysis.
Graph Spectra: Link to Graph spectral analysis.
Help: Link to the help and tutorial of the portal.
Download: The download options for a particular page are shown.
i
Global properties
Nr: Number of nodes in the network. This represents the number of residues in the protein (or complex).
Ne: Number of edges in the network.
D: Shortest path distance between the pair of farthest nodes in the network.
R: Shortest path distance of the centre(s) of the network to the farthest node.
k: Average degree of all the nodes in the network.
l: Average of shortest path between all node pairs in the network.
c: Clustering coefficient of the network.
Network Analysis
View Network: Link to View network.
Node centrality: Link to Node centrality analysis.
Edge centrality: Link to Edge centrality analysis.
Shortest path analysis: Link to Shortest path analysis.
k-clique analysis: Link to k-clique analysis.
Domain view: Link to Multi-domain analysis.
Graph Spectra: Link to Graph spectral analysis.
View network
View type
Network 3D: 3D representation of the network with node coordinates representing the actual
coordinates of the residue.
Contact Map: 2D contact map view.
Distance matrix: 2D distance matrix view.
Highlight selection: Active only for Network 3D view.
Node: On selecting a node in the 3D network view, the node and the corresponding residue in
NGL view are highlighed in red color.
Neighbors: On selecting a node in the 3D network view, the node and the corresponding residue in
NGL view are highlighted in red color. The neighboring nodes in the network view and the corresponding residues in
NGL view are highlighted in yellow color.
Show
All residues:Display all residues and endges between them.
Hydrophobic:Highlight hydrophobic residues and show edges only between them.
Hydrophilic:Highlight hydrophilic residues and show edges only between them.
Charged:Highlight charged residues and show edges only between them.
Structure image: Save the structure image in PNG format.
Network image: Save the network image in PNG or JPEG format.
Node Centrality analysis
Centrality: Option to select centrality from drop down menu.
Sort by: Option to sort the centrality display table based on residue or
centrality.
Generate plot: Button to plot the selected centrality.
Color by: Option to color the nodes in network 3d view.
Default: Nodes are colored based on chain id. Chain 1 is colored blue and Chain 2 as green.
Centrality: Nodes are colored based on selected centrality value.
Hydrophobicity: Nodes are colored based on hydrophobicity value.
Highlight selection: Active for Color by "default".
Node: On selecting a node in the 3D network view, the node and the corresponding residue in
NGL view are highlighed in red color.
Neighbors: On selecting a node in the 3D network view, the node and the corresponding residue in
NGL view are highlighted in red color. The neighboring nodes in the network view and the corresponding residues in
NGL view are highlighted in yellow color.
Structure image Save the structure image in PNG format.
Network image Save the network image in PNG or JPEG format.
Edge Centrality analysis
Centrality: Option to select centrality from drop down menu.
At present, only edge betweenness is displayed.
Structure image Save the structure image in PNG format.
Network image Save the network image in PNG or JPEG format.
Shortest path analysis
Residue 1: Start residue id to be selected from drop down menu.
Residue 2: End residue id to be selected from drop down menu.
Compute shortest path: Button to perform shortest path computation.
Structure image Save the structure image in PNG format.
Network image Save the network image in PNG or JPEG format.
k-clique analysis
Clique size (k): Size of the clique.
Find clique: Perform clique identification at the server.
Structure image Save the structure image in PNG format.
Network image Save the network image in PNG or JPEG format.
Domain view
Number of domains: Number of domains to be highlighted and analysed.
Domain details: Chain id and residue range of each domain.
Color domains Button to color domains.
Structure image Save the structure image in PNG format.
Network image Save the network image in PNG or JPEG format.
Graph Spectra
Eigen spectra: Option to select 1) Principal eigenvector component of Adjacency matrix, or 2) Eigen vector correspondin second smallest eigen value of Laplacian matrix (SSEVL)
Sort by: Option to sort result table based on residue or eigenvector component.
Color by: Option to color the nodes in network 3d view.
Default: Nodes are colored based on chain id. Chain 1 is colored blue and Chain 2 as green.
Eigen spectra: Nodes are colored based on selected eigenvector component.
Hydrophobicity: Nodes are colored based on hydrophobicity value.
Highlight selection: Active for Color by "default".
Node: On selecting a node in the 3D network view, the node and the corresponding residue in
NGL view are highlighed in red color.
Neighbors: On selecting a node in the 3D network view, the node and the corresponding residue in
NGL view are highlighted in red color. The neighboring nodes in the network view and the corresponding residues in
NGL view are highlighted in yellow color.
Structure image Save the structure image in PNG format.
Network image Save the network image in PNG or JPEG format.
Connected Component analysis
Component type: Choose the network to be analysed: Protein-Phosphate Network, Protein-Sugar Network or Protein-Base Network.
Connected Components: Displays all the connected components of the chosen network. Clicking on the radio-button of a particular connected component highlights the nodes and edges of that connected component in both the Network View and the Structure View.
Save Structure: Save the structure image in PNG format.
Save Network: Save the network image in PNG or JPEG format.
Hub analysis
Component type: Choose the network to be analysed: Protein-Phosphate Network, Protein-Sugar Network or Protein-Base Network.
Degree cutoff: Choose the degree cutoff for defining the hubs. It represents the minimum no. of edges required for a node to be defined as a hub. Choosing a degree cutoff highlights the hubs in both the Network View and the Structure View accordingly with red color.
Hubs: Displays all the hubs of the chosen network and their degree.
Save Structure: Save the structure image in PNG format.
Save Network: Save the network image in PNG or JPEG format.
Bulk execution
Instructions for bulk execution using website
1. Upload a tab separated text file containing PDB Ids and chain Ids. Each line of the text file should contain PDB Id followed by chain id. Sample.txt
2. Select the analysis type that has to be carried out for all the structures.
3. Select the network construction method and the cutoff values.
Instructions for bulk execution using API
2. Download and execute API script: python script.
3. Command line arguments for the API script:
(i) pdb_list: A tab separated file with PDB id's and chain id's sample.txt
(ii) graph type: calpha, cbeta, IS (interaction strength), APC (atom pair contact), centroid
(iii) weight: weighted or unweighetd
(iv) lower cutoff: lower cutoff for network (0 for interaction strength network)
(v) upper cutoff: upper cutoff for network and Interaction strength threshold (%) for interaction strength network
(vi) residue separation
(vii) type of analysis: edgelist, centrality, global (global centraliy measures).
4. Output: A zip file will be downloaded in the working directory.
Sample execution: python2.7 api_bulk.py sample.txt calpha unweighted 0 7 1 edgelist
