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<div align="center"><h1>AminoNet</h1></div>
<div align="center"><h3>Version 1.0</h3></div>
<div align="center"><h2>Documentation</h2></div>
<a name=introduction></a>
<div align="left"><h3>Introduction</h3></div>
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 C&alpha; atoms as well as all atoms
of an amino acid as a node. If any two nodes (C&alpha; 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.
<a name=downloads></a>
<div align="left"><h3>Downloads</h3></div>
Get it <a href="http://www.bioinformatics.org/project/filelist.php?group_id=810" title=""target =_new>here</a>.
<a name=installation></a>

<div align="left"><h3>Installation</h3></div>
System Requirments:<br>
<u><i><font color=red>To use AminoNet jre version 1.6 or latter is required</font></i></u><br> 
Copy both the files (AminoNet.jar and AminoNet.html) into a directory and open the html file with a java enabled web browser.
<div align="left"><h2>Tutorial</h2></div>
<div align="left"><h3>Menu</h3></div>

<img src="image/select.jpg" border="0" alt="" align="middle">
<hr />
<a name=toppanel></a>

<div align="left"><h3>Top Panel</h3></div>
In the top panel there is a check box where users have to select C&alpha; only if he wants to construct 
the unweighted network. The default is the construction of a weighted network. 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. <br clear="all">
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. 

<br clear="all">
In the next text box, user can enter a cut-off value of his choice
 or use the default value (5&Aring;). Then press enter to calculate the values of different network parameters.<br clear="all">
There are also check boxes where user can select the hydrophobic, hydrophilic, charged and all amino acids networks.


<hr /><a name=lodingfile></a>

<div align="left"><h3>Loading File</h3></div>
Loading a protein can be done in two ways
 <ol>To load a file from the local computer
	<li>click file --> open --> (choose a pdb file) --> open</li>
	<div align="center">OR</div>
	To fetch and load a file from www.pdb.org  
	<li>type the PDB ID of the query protein with or without .pdb extension and press enter</li>
</ol> 
<hr />
<a name=residues></a> 

<div align="left"><h3>Residues Tab</h3></div>
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 to get this information. 
<p></p>
<img src="image/residues.jpg"  border="0" alt="" align="middle">
<hr /><a name=values></a>

<div align="left"><h3>Values Tab</h3></div>
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.
<p></p>
<img src="image/values.jpg"  border="0" alt="" align="middle">
<hr /><a name=graphs></a>

<div align="left"><h3>Graphs Tab</h3></div>
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.
<p></p>
<img src="image/graphs.jpg"  border="0" alt="" align="middle">
<hr /><a name=networks></a>

<div align="left"><h3>Networks Tab</h3></div>
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.
<p></p>
<img src="image/networks.jpg"  border="0" alt="">
<hr /><a name=uservalues></a>

<div align="left"><h3>User Values Tab</h3></div>
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.
<br />
<p></p><img src="image/uservalues.jpg"  border="0" alt="" align="middle">
<hr /><a name=twodviews></a>

<div align="left"><h3>2D View Tab</h3></div>
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.
<p></p><img src="image/ranges.jpg"  border="0" alt="" align="middle">

<hr />
<a name=ranks></a>

<div align="left"><h3>Ranks Tab</h3></div>
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. 
<p></p>
<img src="image/ranks.jpg"  border="0" alt="" align="middle">

<hr />
<a name=anotations></a>

<div align="left"><h3>Annotations</h3></div>
Annotations used in AminoNet tool 
<ul>

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


    
<hr />      
<a name=references></a>

<div align="left"><h3>References</h3></div>
<ol>
	<li>Aftabuddin,M. and Kundu,S. (2006) Weighted and unweighted network of amino acids within protein, <i> Physica A</i>,  369, 895-904.</li>
	<li>Aftabuddin,M. and Kundu,S. (2007) Hydrophobic, hydrophilic and charged amino acids' networks within Protein,  Biophysical J.,  93,  225-231.</li>
	<li>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.</li>
	<li>Bagler,G. and Sinha, S. (2005)Network properties of protein Structures,  Physica A,  346, 27-33.</li>
	<li>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.</li>
	<li>Greene,L.H. and Higman,V.A. (2003) Uncovering network systems within protein structures,  J. Mol. Biol.,  334, 781-791.</li>
	<li>Kundu,S. (2005). Amino acid network within protein.  Physica A,  346, 104-109.</li>

</ol>

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