{% extends "base.html" %}

{% load i18n lazysignup_tags %}
{% block content %}

<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".
Postprocessing do not count to 100%. 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>
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            style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
    
    <div class="hiders" style="display:none" >
<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>

<h4><li>Molecular dynamics of IGG-binding domain from streptococcal protein G
(PDB code:1IGD) starting from the native structure</h4>
<div>
    <fieldset class="majorpoints">
        <legend class="majorpointslegend"
            style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
    
    <div class="hiders" style="display:none" >

<p>
<img src="static/md.png" style="border:2px solid blueviolet">
<p>
The results of md simulations show temperature histogram, 
potential energy changes, movie generated from trajectory,
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>
<h4><li>
Replica exchange molecular dynamics of Trp-Cage miniprotein (PDB
code:1L2Y) starting from the extended chain </h4>  
<div>
    <fieldset class="majorpoints">
        <legend class="majorpointslegend"
            style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
    
    <div class="hiders" style="display:none" >
<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. Models are shown using NGL Viewer.
PDB files can be downloaded by clicking on the <i>Download</i> button.
<p>
<a href="static/remd9.png"><img src="static/remd9.png" width="300px"></a>

<p>


</div>
</div>
</ol>
<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): 
<ol>
<h4><li>
Minimization of the P8MTCP1 disulfide-bonded helical hairpin miniprotein
(PDB code: 1EI0).</h4>
<div>
    <fieldset class="majorpoints">
        <legend class="majorpointslegend"
            style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
    
    <div class="hiders" style="display:none" >
<p>
In this example the PDB code of selected protein (1EI0) and opt-wtfsa-2
force field are selected:  
<p>
<img src="static/min_adv.png" style="border:2px solid blueviolet">

The results of local minimizations show the UNRES model of 1EI0 protein
with two dissulfide bonds as read from pdb, 
its total UNRES energy and overlap on starting structure:
<p>
<a href="static/min_adv1.png"><img src="static/min_adv1.png" width="300px"></a>
<a href="static/min_adv2.png"><img src="static/min_adv2.png" width="300px"></a>
<a href="static/min_adv3.png"><img src="static/min_adv3.png" width="300px"></a>

    </div>
</div>

<h4><li>
Canonical MD simulations of Trp-Cage miniprotein (PDB code:1L2Y) 
starting from extended chain.</h4>
<div>
    <fieldset class="majorpoints">
        <legend class="majorpointslegend"
            style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
    
    <div class="hiders" style="display:none" >
In this example the PDB code of selected protein (1L2Y) and 
option to write trajectory as pdb are selected, saving trajectory 
as pdb allows its 3D visualisation in NGL Viewer in addtion to
movie which is always generated from the MD trajectory 
<p>
<img src="static/md_adv.png" style="border:2px solid blueviolet">
<br>
...
<br>
<img src="static/md_adv0.png" style="border:2px solid blueviolet">
<p>
The results of md simulations show temperature histogram, 
potential energy changes, movie generated from trajectory,
trajectory visualization in NGL Viewer,
evolution of radius of gyration,
RMSD, fraction of native contacts:
<p>
<a href="static/md_adv1.png"><img src="static/md_adv1.png" width="300px"></a>
<a href="static/md_adv2.png"><img src="static/md_adv2.png" width="300px"></a>
<a href="static/md_adv3.png"><img src="static/md_adv3.png" width="300px"></a>
<a href="static/md_adv4.png"><img src="static/md_adv4.png" width="300px"></a>
<a href="static/md_adv5.png"><img src="static/md_adv5.png" width="300px"></a>
<a href="static/md_adv6.png"><img src="static/md_adv6.png" width="300px"></a>
<a href="static/md_adv7.png"><img src="static/md_adv7.png" width="300px"></a>
<p>
Evolution of RMSD and fraction of native contacts 
is shown only when reference structure is provided as in this example.
The CA fluctuations are not analyzed for start from the extended structure
because of large scale conformational changes during folding.

    </div>
</div>


<h4><li>
MREMD simulations of 5G3Q:B (CASP12 target T0882)</h4>
 
<div>
    <fieldset class="majorpoints">
        <legend class="majorpointslegend"
            style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
    
    <div class="hiders" style="display:none" >
This simulation starts from extended chain, 2000000 steps for each of 16
replicas (8 temperatures with multiplexing 2)
are run and secondary structure restraints predicted by PSIPRED and 
obtained at the CASP12 time when the experimental 5G3Q structure
was not included in the PDB database are used. Berendsen thermostat
and clustering temperature 290K are selected. 
This is a full-blown structure-prediction run, but shorter
in comparison to UNRES runs during CASP.

<p>
<img src="static/remd_adv.png" style="border:2px solid blueviolet">
<br>
...
<br>
<img src="static/remd_adv01.png" style="border:2px solid blueviolet">
<br>
...
<br>
<img src="static/remd_adv02.png" style="border:2px solid blueviolet">
<br>
...
<br>
<img src="static/remd_adv03.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/remd_adv1.png"><img src="static/remd_adv1.png" width="300px"></a>
<a href="static/remd_adv2.png"><img src="static/remd_adv2.png" width="300px"></a>
<a href="static/remd_adv3.png"><img src="static/remd_adv3.png" width="300px"></a>
<a href="static/remd_adv4.png"><img src="static/remd_adv4.png" width="300px"></a>
<a href="static/remd_adv5.png"><img src="static/remd_adv5.png" width="300px"></a>
<a href="static/remd_adv6.png"><img src="static/remd_adv6.png" width="300px"></a>
<a href="static/remd_adv7.png"><img src="static/remd_adv7.png" width="300px"></a>
<a href="static/remd_adv8.png"><img src="static/remd_adv8.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. Models are shown using NGL Viewer.
PDB files can be downloaded by clicking on the <i>Download</i> button.
RMSD of model 1 
from the experimental structure is 3.6 A and 
the GDT TS is 58.8 %

<p>
<a href="static/remd_adv9.png"><img src="static/remd_adv9.png" width="300px"></a>

<p>


    </div>
</div>


<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 1</i> button in advanced mode)
</h4>  
<div>
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        <legend class="majorpointslegend"
            style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
    
    <div class="hiders" style="display:none" >
<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>

<h4><li>
Distance distribution restrained (real SAXS data)
replica exchange molecular dynamics of 
the central portion of Factor H (PDB code:2KMS).
<br>
(Use <i>Load example SAXS 2</i> button in advanced mode)
</h4>  
<div>
    <fieldset class="majorpoints">
        <legend class="majorpointslegend"
            style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
    
    <div class="hiders" style="display:none" >
REMD simulation starts from the experimental NMR structure. Secondary
structure restraints are used. Only short (50 energy evaluations)
initial minimization is requested.
The SASDA25 entry of the SASBDB is used for SAXS distance distribution.

<img src="static/saxs2_1.png" style="border:2px solid blueviolet">
<br>
...
<br>
<img src="static/saxs2_2.png" style="border:2px solid blueviolet">
<br>
...
<br>
<img src="static/saxs2_3.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/sasx2_4.png"><img src="static/saxs2_4.png" width="300px"></a>
<a href="static/saxs2_5.png"><img src="static/saxs2_5.png" width="300px"></a>
<a href="static/saxs2_6.png"><img src="static/saxs2_6.png" width="300px"></a>
<a href="static/saxs2_7.png"><img src="static/saxs2_7.png" width="300px"></a>
<a href="static/saxs2_8.png"><img src="static/saxs2_8.png" width="300px"></a>
<a href="static/saxs2_9.png"><img src="static/saxs2_9.png" width="300px"></a>
<a href="static/saxs2_10.png"><img src="static/saxs2_10.png" width="300px"></a>
<a href="static/saxs2_11.png"><img src="static/saxs2_11.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. 
In the UNRES calculated
structures, the domains are at a larger angle than
those in the experimental NMR structure.

<p>
<a href="static/saxs2_13.png"><img src="static/saxs2_13.png" width="300px"></a>

<p>
Additionaly the input reference distance distribution and 
distance distributions for 5 final models are plotted.
The distance distribution calculated from the
experimental NMR structure does not fully overlap with that from
SAXS; in particular, the plot calculated from the 2KMS
structure decays to 0 quicker than that from SAXS.
Much better agreement, in
particular in the long-distance part is obtained
for structres from the UNRES simulation.
<p>
<a href="static/saxs2_12.png"><img src="static/saxs2_12.png" width="300px"></a>


</div>

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{% endblock %}