# AminoNet

### Version 2.0

## Documentation

### Introduction

Recently several groups have studied the protein structure networks to understand the topology of interacting amino acids, the key residues for maintaining its structure and function, structural organization and mixing behaviour of the nodes, etc. One can consider only Cα atoms, any other atoms as well as all atoms of an amino acid as a node. If any two nodes (Cα or any atom of an amino acid) are within a cutoff distance, then there is a connection or edges between these two nodes. This web based tool is able to construct and visualize different protein contact networks (unweighted and weighted; long range and short range; hydrophobic, hydrophilic, charged or all amino acids networks) and also able to calculate different topological parameters.The tool calculates the values for the networks(or subnetworks) having atleast 30 nodes.

### Downloads

Get it here.

### Installation

System Requirements:
To use AminoNet jre version 1.6 or latter is required
Copy both the files (AminoNet.jar and AminoNet.html) into a directory and open the html file with a java enabled web browser.

## Tutorial

### Menu

### Top Panel

In the top panel the first dropdown list is for selecting chain of the PDB. The list comes only after a files has been loaded. In the second dropdown list the users have to select Cα or any other atom if he wants to construct the unweighted network. If all is selected from the dropdown list then it will construct unweighted as well as weighted network considering all atoms of an amino acid. There is also a drop down menu from where 'any', 'long' or 'short' range interactions can be chosen. If two residues are at least 10 residues apart in the primary chain then the interaction has been considered as long range interaction, otherwise it is considered as short range interaction.
In the next text box, user have to enter the PDB ID of the query protein. It would automatically fetch the structure of that protein from PDB.
In the next text box, user can enter a cut-off value of his choice or use the default value (5Å). Then press enter to calculate the values of different network parameters.
There are also check boxes where user can select the hydrophobic, hydrophilic, charged and all amino acids networks.

### Loading File

Loading a protein can be done in two ways

To load a file from the local computer
1. click file --> open --> (choose a pdb file) --> open
OR
To fetch and load a file from www.pdb.org
2. type the PDB ID of the query protein with or without .pdb extension and press enter

### Batch Job

The user can also do batch jobs in the AminoNet.

The file format of batch file is
1. To load files from the local computer
One has to write in the first line of the batch file <local> then all the names of the pdb files, one name in each line. i.e.
<local>
2BIB.pdb
1CD8.pdb
1KEK.pdb
The batch file must be kept in a directory where the .pdb files has been saved
2. To load files from www.pdb.org
One has to write in the first line of the batch file <net> then all th e names of the pdb files, one name in each line. i.e.
<net>
2BIB.pdb
1CD8.pdb
1KEK.pdb

click file --> batch --> (choose a batch file) --> open

For both the above cases the output will be automatically saved in a file named outbatch.txt in the diretory contaning the batch file.

### Saving Output

For the single file jobs the values in the 'Values' panel can be saved

click file --> Save... --> (give a file name) --> Save

### Residues Tab

In this tab the residues along with their numbers and chain information present in the protein are shown. On the top right one has to select any or all checkboxes (All, Phobic, Philic and Charged) to get this information.

### Values Tab

In this tab there are four panels. In each panel a drop down list is given, where the cluster numbers are shown if the cluster size is at least 30. In this panel the values of different network parameters are shown for the chosen cluster. Also residue information is shown when the mouse pointer is kept on the words "Cluster no." at the left of the drop down box.

### Graphs Tab

One can see different graphs type (i.e. P(k) vs k, S(k) vs k, C(k) vs k, Cw(k) vs k) for the cluster chosen in the values tab.

### Networks Tab

In the networks tab one can choose any option from the drop-down list to view a particular network. Also one can see the labels by selecting the 'Show Label' check box. The network can be rotated by dragging the mouse on the panel. It can be zoomed using the right mouse button and can be shifted by holding the shift key while dragging. Using the 'Reset' button the graph can be viewed in its initial position.

### User Values Tab

In the 'User Values' tab one can see values related to a particular residue. In the 'Residue' text box one has to enter a residue number for which he wants to know the properties. The properties will be calculated for the cluster chosen in the 'Values' tab.

### 2D View Tab

In this tab the residues are represented according to the primary chain circularly starting from the extreme right moving clockwise. A line is shown if there is a connection between any two residues (other than peptide bonds). Here, one can also select "All","Hydrophobic", "Hydrophilic" or "Charged". One can also get the 2D view of any, long or short range networks selceting the proper option. The check box "Show Label" will provide the residue numbers in 2D view. The residue numbers are shown with a gap of 30 residues statring from the first residue present in the pdb file. The Circular graph can be zoomed holding the right mouse button while dragging. Also it can be shifted holding shift key and left mouse button while dragging.

### Ranks Tab

In this tab the Z Scores of the nodes are shown. The columns can be sorted in ascending order and in decending order by clicking the column headers. This needs huge computational time. The present web server do that for a network having maximum 100 residues. However, one can do the same for larger networks in the standalone version. In standalone version, one may change the value of network size (maxZSize) in AminoNet.html file.

### Annotations

Annotations used in AminoNet tool

- N - number of nodes (residues) in the network
- K - degree of the i-th node
- <K> - average degree of nodes in the network
- S - strength of the i-th node
- <S> - average strength of nodes in the network
- Lres - average of shortest paths from the i-th node to all other nodes of the network
- Cres - reciprocal of Lres ie. closeness centrality of a node
- L - characteristic path length of network
- Lr - characteristic path length of random network (=ln N / ln <K>)
- Cr - clustering coefficient of random network (= <K> / N )
- C - clustering coefficient of network
- Cw - weighted clustering coefficient of network
- r - correlation coefficient of network signifing the amino acid mixing behavior
- p - the ratio of average clustering coefficient of the network to that of the corresponding random network (= <C> / <Cr> )
- q - the ratio of characteristic path length of the network to that of the corresponding random network (= <L> / <Lr> )
- <Wij> - average weight (It is the average of the numbers of all possible interactions of all possible pairs of nodes)
- Z Score - it helps to find the statistically significant central nodes of a network

For further details see the references

### References

1. Aftabuddin,M. and Kundu,S. (2006) Weighted and unweighted network of amino acids within protein, Physica A, 369, 895-904.
2. Aftabuddin,M. and Kundu,S. (2007) Hydrophobic, hydrophilic and charged amino acids' networks within Protein, Biophysical J., 93, 225-231.
3. Amitai,G., Shemesh,A., Sitbon,E., Shklar,M., Netanely,D., Venger,I. and Pietrokovski,S. (2004) Network analysis of protein structures identifies functional residues, J Mol Biol, 344, 1135-46.
4. Bagler,G. and Sinha, S. (2005)Network properties of protein Structures, Physica A, 346, 27-33.
5. del Sol,A., Fujihashi,H., Amoros,D. and Nussinov,R. (2006) Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol Syst Biol., 2:2006.0019. Epub 2006 May 2.
6. Greene,L.H. and Higman,V.A. (2003) Uncovering network systems within protein structures, J. Mol. Biol., 334, 781-791.
7. Kundu,S. (2005). Amino acid network within protein. Physica A, 346, 104-109.