{% extends "base.html" %}

{% load i18n lazysignup_tags %}
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<h4>
In order to submit a job you need to provide its name:</h4>
<p>
<img src="static/name.png" style="border:2px solid blueviolet">
<p>
UNRES server allows three types of simulations: 
local minimization, molecular dynamics and replica exchange molecular dynamics:
<p>
<img src="static/types.png" style="border:2px solid blueviolet">
<p>
Use "Save & submit" button to start calculations.
<img src="static/submit.png" style="border:2px solid blueviolet">
<p>
Use "Refresh" button to check the status of simulation:
<p>
<img src="static/refresh.png" style="border:2px solid blueviolet">
<p>
until
<img src="static/done.png" style="border:2px solid blueviolet">
<p>
The job status information will start from the "waiting in the queue to
start", then "running" and finally "postprocessing" before "done".
Autorefresh is active every 30 sec.
<p>
Any single job can by accessed later using the adress of the web page
displayed after job submission: 
http://unres-server.chem.ug.edu.pl/details1/570cf15fc638493893ece1f011ea0182/984/
<br>
Registered users can save all their jobs and access them  after login.
<p>
<h4>You can use "Load example data" button before submitting calculations 
to try examples listed below:</h4>
<p>
<ol>
<h4><li>Local minimization of protein A (PDB code:1BDD) structure</h4>
<div>
    <fieldset class="majorpoints">
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<p>
In this example only the PDB code of selected protein (1BDD) is provided
<p>
<img src="static/min.png" style="border:2px solid blueviolet">


The results of local minimizations show the UNRES model of 1BDD protein, 
its total UNRES energy and overlap on starting structure:
<p>
<a href="static/min1.png"><img src="static/min1.png" width="300px"></a>
<a href="static/min2.png"><img src="static/min2.png" width="300px"></a>
<p>
All files generated during calculations 
can be viewed/download by clicking on "Directory" link.
</div>
</div>

<hr>
<h4><li>Molecular dynamics of IGG-binding domain from streptococcal protein G
(PDB code:1IGD) starting from the native structure</h4>
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<p>
<img src="static/md.png" style="border:2px solid blueviolet">
<p>
The results of md simulations show temperature histogram, 
potential energy changes, evolution of radius of gyration,
RMSD, fraction of native contacts, and CA fluctuations:
<p>
<a href="static/md1.png"><img src="static/md1.png" width="300px"></a>
<a href="static/md2.png"><img src="static/md2.png" width="300px"></a>
<a href="static/md3.png"><img src="static/md3.png" width="300px"></a>
<a href="static/md4.png"><img src="static/md4.png" width="300px"></a>
<a href="static/md5.png"><img src="static/md5.png" width="300px"></a>
<a href="static/md6.png"><img src="static/md6.png" width="300px"></a>
<a href="static/md7.png"><img src="static/md7.png" width="300px"></a>
<a href="static/md8.png"><img src="static/md8.png" width="300px"></a>
<p>
Evolution of RMSD, fraction of native contacts and 
comparison of CA fluctuations to Bfactor is presented
only when reference structure is provided as in this example.
</div>
</div>
<hr>
<h4><li>
Replica exchange molecular dynamics of Trp-Cage miniprotein (PDB
code:1L2Y) starting from the extended chain </h4>  
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<img src="static/remd.png" style="border:2px solid blueviolet">
<p>

Plots of histograms of UNRES energy for each temperature, and
energy vs temperature are presented.
The weighted histogram analysis (WHAM) is applied to compute the
probabilities of the obtained conformations to occur at particular
temperatures, plots of heat capacity and average RMSD as a functions
of temperature are shown. Replica exchanges are analyzed.
<p>
<a href="static/remd1.png"><img src="static/remd1.png" width="300px"></a>
<a href="static/remd2.png"><img src="static/remd2.png" width="300px"></a>
<a href="static/remd3.png"><img src="static/remd3.png" width="300px"></a>
<a href="static/remd4.png"><img src="static/remd4.png" width="300px"></a>
<a href="static/remd5.png"><img src="static/remd5.png" width="300px"></a>
<a href="static/remd6.png"><img src="static/remd6.png" width="300px"></a>
<a href="static/remd7.png"><img src="static/remd7.png" width="300px"></a>
<a href="static/remd8.png"><img src="static/remd8.png" width="300px"></a>
<p>
Finally cluster analysis is performed to select 5 families of conformations,
and representative model from each family is converted to all-atom
and refined. PDB files can be downloaded by clicking on the picture.
<p>
<a href="static/remd9.png"><img src="static/remd9.png" width="300px"></a>

<p>


</div>
</div>
<hr>
Advanced mode allows for changes of more parameters of each type of
simulation. Separate examples are provided (use <i>Load example data</i> button as
in Basic mode): minimization of 1EI0 with
dissulfide bonds, MD simulations of 1L2Y starting from extended chain
and multiplexed replica exchange simulations of 5G3Q:B (CASP12 target T0882) 
starting form extended chain with secondary structure restraints predicted
by PSIPRED and Berendsen thermostat.

<hr>
<h4><li>
Distance distribution restrained (simulated SAXS data)
replica exchange molecular dynamics of 
Bacteriocin CbnXY (PDB code:5UJQ) starting from the extended chain.
<br>
(Use <i>Load example SAXS data</i> button in advanced mode)
</h4>  
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<img src="static/saxs1.png" style="border:2px solid blueviolet">
<br>
...
<br>
<img src="static/saxs2.png" style="border:2px solid blueviolet">
<p>

Plots of histograms of UNRES energy for each temperature, and
energy vs temperature are presented.
The weighted histogram analysis (WHAM) is applied to compute the
probabilities of the obtained conformations to occur at particular
temperatures, plots of heat capacity and average RMSD as a functions
of temperature are shown. Replica exchanges are analyzed.
<p>
<a href="static/saxs3.png"><img src="static/saxs3.png" width="300px"></a>
<a href="static/sasx4.png"><img src="static/saxs4.png" width="300px"></a>
<a href="static/saxs5.png"><img src="static/saxs5.png" width="300px"></a>
<a href="static/saxs6.png"><img src="static/saxs6.png" width="300px"></a>
<a href="static/saxs7.png"><img src="static/saxs7.png" width="300px"></a>
<a href="static/saxs8.png"><img src="static/saxs8.png" width="300px"></a>
<a href="static/saxs9.png"><img src="static/saxs9.png" width="300px"></a>
<a href="static/saxs10.png"><img src="static/saxs10.png" width="300px"></a>
<p>
Finally cluster analysis is performed to select 5 families of conformations,
and representative model from each family is converted to all-atom
and refined. 
<p>
<a href="static/saxs12.png"><img src="static/saxs12.png" width="300px"></a>

<p>
Additionaly the input reference distance distribution and 
distance distributions for 5 final models are plotted.
<p>
<a href="static/saxs11.png"><img src="static/saxs11.png" width="300px"></a>


</div>
</div>


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